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- PDB-5xlh: Crystal structure of aerobically purified and aerobically crystal... -

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Basic information

Entry
Database: PDB / ID: 5xlh
TitleCrystal structure of aerobically purified and aerobically crystallized for 12weeks D. vulgaris Miyazaki F [NiFe]-hydrogenase
Components(Periplasmic [NiFe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [NiFe]-hydrogenase D. vulgaris
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / Periplasmic [NiFe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNishikawa, K. / Mochida, S. / Hiromoto, T. / Shibata, N. / Higuchi, Y.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Authors: Nishikawa, K. / Mochida, S. / Hiromoto, T. / Shibata, N. / Higuchi, Y.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Periplasmic [NiFe] hydrogenase small subunit
L: Periplasmic [NiFe] hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1208
Polymers89,7682
Non-polymers1,3526
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-114 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 98.440, 126.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Periplasmic [NiFe] hydrogenase ... , 2 types, 2 molecules SL

#1: Protein Periplasmic [NiFe] hydrogenase small subunit / NiFe hydrogenlyase small chain


Mass: 28789.746 Da / Num. of mol.: 1 / Fragment: UNP residues 51-317 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) (bacteria)
Strain: Miyazaki F / DSM 19637 / References: UniProt: P21853, cytochrome-c3 hydrogenase
#2: Protein Periplasmic [NiFe] hydrogenase large subunit / NiFe hydrogenlyase large chain


Mass: 60978.453 Da / Num. of mol.: 1 / Fragment: UNP residues 1-552 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) (bacteria)
Strain: Miyazaki F / DSM 19637 / References: UniProt: P21852, cytochrome-c3 hydrogenase

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Non-polymers , 6 types, 757 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe3S4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 120962 / % possible obs: 99.7 % / Redundancy: 5.3 % / Net I/σ(I): 4.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→32.292 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 3167 4.99 %
Rwork0.1671 --
obs0.1692 63427 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→32.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6170 0 41 751 6962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016455
X-RAY DIFFRACTIONf_angle_d1.3788812
X-RAY DIFFRACTIONf_dihedral_angle_d15.9192328
X-RAY DIFFRACTIONf_chiral_restr0.079955
X-RAY DIFFRACTIONf_plane_restr0.0061147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95880.27511350.24242575X-RAY DIFFRACTION100
1.9588-1.98940.2831360.24142575X-RAY DIFFRACTION100
1.9894-2.0220.27811370.22992613X-RAY DIFFRACTION100
2.022-2.05680.27121350.22452550X-RAY DIFFRACTION100
2.0568-2.09420.27941370.2112613X-RAY DIFFRACTION100
2.0942-2.13450.25511350.20592569X-RAY DIFFRACTION100
2.1345-2.17810.26691360.20622598X-RAY DIFFRACTION100
2.1781-2.22540.23941370.19632601X-RAY DIFFRACTION100
2.2254-2.27720.26841370.19822585X-RAY DIFFRACTION100
2.2772-2.33410.22371360.18462589X-RAY DIFFRACTION100
2.3341-2.39720.24331380.16832624X-RAY DIFFRACTION100
2.3972-2.46770.22481370.15892599X-RAY DIFFRACTION100
2.4677-2.54730.19651370.16262603X-RAY DIFFRACTION100
2.5473-2.63830.21141370.16122610X-RAY DIFFRACTION100
2.6383-2.74390.22831370.16592599X-RAY DIFFRACTION100
2.7439-2.86870.23451380.16522628X-RAY DIFFRACTION100
2.8687-3.01990.20211390.15362632X-RAY DIFFRACTION100
3.0199-3.20890.18831390.14912639X-RAY DIFFRACTION100
3.2089-3.45640.16611380.14122621X-RAY DIFFRACTION100
3.4564-3.80380.18441400.13952658X-RAY DIFFRACTION100
3.8038-4.3530.16031410.13692676X-RAY DIFFRACTION100
4.353-5.480.17421390.14682693X-RAY DIFFRACTION99
5.48-32.2970.19091460.17262810X-RAY DIFFRACTION99

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