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Acta Cryst. (2014). A70, C1201
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It is important for understanding the electron transfer reaction to include the information about valence shell electrons and hydrogen atoms into crystal structure refinement. High-potential iron-sulfur protein (HiPIP) possesses a Fe4S4 cluster which exhibits +2/+3 redox states and acts as an electron carrier from cytochrome bc1 complex to the reaction center complex in photosynthetic purple bacteria. We have reported the X-ray crystal structure of HiPIP from Thermochtomatium tepidum at 0.72 Å resolution (1). Recently, we have successfully collected 0.48 Å resolution data of HiPIP using high-energy X-rays (31 keV) in BL41XU beamline of SPring-8. We performed multipolar refinement with the MoPro program (2) to consider valence shell electrons in the structure refinement of HiPIP. Refinement of multipolar parameters was applied to atoms of single conformational residues, water molecules with two hydrogen atoms, and the Fe4S4 cluster. After multipolar refinement, the deformation map clearly displays the distribution of valence shell electrons such as lone-pair electrons of carbonyl oxygen atoms, bonding electrons in aromatic rings, and d-orbital electrons of Fe atoms in the Fe4S4 cluster. The deformation map also indicates electrostatic interactions between the S atoms of Fe4S4-(Cys-Sγ)4 and protein environment. In addition, we performed preliminary neutron diffraction experiment at iBIX beamline of Japan Proton Accelerator Research Complex (J-PARC) and observed diffraction spots up to 1.17 Å resolution using HiPIP crystal with the size of 2.3 mm3. In the multipolar refinement, the positions of hydrogen atoms were fixed to the standard bond distances derived from neutron crystal structures of small molecules and atomic displacement parameters of hydrogen atoms were constrained to 1.2 or 1.5 fold of their root atoms. Therefore, a high resolution neutron structure of HiPIP will improve the results obtained from the multipolar refinement.

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Acta Cryst. (2014). A70, C1216
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Elastase is a serine protease classified in the chymotrypsin family, and is attractive target for studies of structure based drug design (SBDD). The structural information including hydrogen positions and hydration will help us to further elucidate the catalytic mechanism of serine protease. To obtain such structural information, we performed the neutron structure analyses of porcine pancreatic elastase (PPE) with and without its inhibitor using diffraction data obtained at a BIX-3 diffractometer in the research reactor JRR-3. The PPE structure in complex with a peptidic inhibitor, which was used to mimic the tetrahedral intermediate state, was determined to 1.65 Å resolution [1]. His57, Asp102, and Ser195 (chymotrypsin numbering) compose the "catalytic triad" conserved in the active site of serine protease. The complex structure determined by neutron crystallography shows that the hydrogen bond between His57 and Asp102 is essentially short but conventional hydrogen bond, not a low-barrier hydrogen bond. In addition, this neutron structure clearly shows that the oxygen of oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the oxyanion hole in stabilizing the intermediate in catalysis. The neutron structure of PPE without inhibitor determined to 1.9 Å resolution shows that a water molecule and hydroxyl group of Ser195 block to two backbone amides of Gly193 and Ser195, which form oxyanion hole, respectively. This structural information allows us to understand the role of resting state upon the catalytic reaction. Furthermore, the structural change of the active site residues including hydration structure obtained from the comparison between structures with and without inhibitor may help designing potent inhibitors by SBDD.

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Acta Cryst. (2014). A70, C1218
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Phytobilins are linear tetrapyrrole compounds used as chromophore for light harvesting and photoreceptor proteins in higher plants, algae, and cyanobacteria. Phytobilins are synthesized from biliverdin IX(alpha) (BV). Phycocianobilin:oxidoreductase (PcyA) is an enzyme to produce phycocyanobilin (PCB) used as chromophore for light harvesting and photoreceptor proteins. PcyA is unique because it catalyzes the reduction of BV by two sequential steps; the first step is the reduction of the vinyl of the BV D-ring to produce 18(1)-18(2)-dihydrobiliverdin (18EtBV), and the second step is the reduction of the A-ring. In these reduction steps, four hydrogen atoms are delivered to BV. The earlier studies showed that the carboxyl group of Asp105 showed dual conformations. This has been attributed to the difference of its protonation states. The catalytically essential His88 was suggested to be protonated (i. e. His88 is a proton donor) to donate the proton to BV. BVH+ (N-protonated) state, in which four pyrrole N atoms of BV were fully protonated, was proposed to be partially formed when BV was bound to PcyA. Further, another tautomeric BVH+ state in which three of four pyrrole N atoms of BV were protonated and the lactam (C=O) group of BV D-ring was protonated as lactim (C-OH; O-protonated) was proposed. Additionally, newly identified water molecule near BV has been suggested to be a proton donor. To elucidate the H atom positions of these molecules, we determined the neutron crystal structure of the PcyA-BV complex at 1.95 Å resolution. Crystal with approximately 2.2 X 1.8 X 0.8 mm3 size, which was soaked into the deuterium-exchanged crystallization solution, was used in the diffraction experiment. The neutron diffraction intensity data was collected using IBARAKI Biological Crystal Diffractometer (iBIX) in J-PARC. In this conference, we report the protonation states of catalytically important residues and BV as well as orientations of water molecules in the PcyA-BV complex.

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Acta Cryst. (2014). A70, C1746
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The structural information of hydrogen atoms and hydration waters obtained by neutron protein crystallography is expected to contribute to elucidation of protein function and its improvement. However, many proteins, especially membrane proteins and protein complexes, have larger molecular weight and then unit cells of their crystals have larger volume, which is out of range of measurable unit cell volume for conventional diffractometers. Therefore, our group had designed the diffractometer which can cover such crystals with large unit cell volume (target lattice length: 250 Å). This diffractometer is dedicated for protein single crystals and has been proposed to be installed at J-PARC (Japan Proton Accelerator Research Complex). Larger unit cell volume causes a problem to separate spots closer to each other in spatial as well as time dimension in diffraction images. Therefore, our proposed diffractometer adopts longer camera distance (L2 = 800mm) and selects decoupled hydrogen moderator as neutron source which has shorter pulse width. Under the conditions that L1 is 33.5m, beam divergence 0.40 and crystal edge size 2mm, this diffractometer is estimated to be able to resolves spots diffracted from crystals with a lattice length of 220 Å in each axis at d-space of 2.0 Å. In order to cover large neutron detecting area due to long camera distance, novel large-area detector (larger than 300mm × 300mm) with a spatial resolution of better than 2.5mm is under development. More than 40 these detectors plan to be installed, providing the total solid angle coverage of larger than 33%. For neutron guide, ellipsoidal supermirror is considered to be adopted to increase neutron flux at the sample position. The final gain factor of this diffractometer is estimated to be about 20 or larger as compared with BIX-3/4 diffractometers operated in the research reactor JRR-3 at JAEA (Japan Atomic Energy Agency) [1,2].
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