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- PDB-5xf9: Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-... -

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Basic information

Entry
Database: PDB / ID: 5xf9
TitleCrystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state
Components(NAD-reducing ...) x 4
KeywordsOXIDOREDUCTASE / hydrogenase / Ni-Fe / Fe-S
Function / homology
Function and homology information


ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / catalytic complex / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
NAD-reducing hydrogenase, HoxS gamma subunit / 4Fe-4S single cluster domain / 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 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / 2Fe-2S iron-sulfur cluster binding domain ...NAD-reducing hydrogenase, HoxS gamma subunit / 4Fe-4S single cluster domain / 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 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NICKEL (III) ION / CARBONMONOXIDE-(DICYANO) IRON / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / HoxF / HoxY / HoxU / HoxH
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsShomura, Y. / Taketa, M. / Nakashima, H. / Tai, H. / Nakagawa, H. / Ikeda, Y. / Ishii, M. / Igarashi, Y. / Nishihara, H. / Yoon, K.S. ...Shomura, Y. / Taketa, M. / Nakashima, H. / Tai, H. / Nakagawa, H. / Ikeda, Y. / Ishii, M. / Igarashi, Y. / Nishihara, H. / Yoon, K.S. / Ogo, S. / Hirota, S. / Higuchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JST CRESTJPMJCR12M4 Japan
CitationJournal: Science / Year: 2017
Title: Structural basis of the redox switches in the NAD(+)-reducing soluble [NiFe]-hydrogenase
Authors: Shomura, Y. / Taketa, M. / Nakashima, H. / Tai, H. / Nakagawa, H. / Ikeda, Y. / Ishii, M. / Igarashi, Y. / Nishihara, H. / Yoon, K.S. / Ogo, S. / Hirota, S. / Higuchi, Y.
History
DepositionApr 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 20, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-reducing hydrogenase
B: NAD-reducing hydrogenase
C: NAD-reducing hydrogenase
D: NAD-reducing hydrogenase
E: NAD-reducing hydrogenase
F: NAD-reducing hydrogenase
G: NAD-reducing hydrogenase
H: NAD-reducing hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,21826
Polymers326,7028
Non-polymers4,51518
Water13,836768
1
A: NAD-reducing hydrogenase
B: NAD-reducing hydrogenase
C: NAD-reducing hydrogenase
D: NAD-reducing hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,60913
Polymers163,3514
Non-polymers2,2589
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16720 Å2
ΔGint-188 kcal/mol
Surface area47020 Å2
MethodPISA
2
E: NAD-reducing hydrogenase
F: NAD-reducing hydrogenase
G: NAD-reducing hydrogenase
H: NAD-reducing hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,60913
Polymers163,3514
Non-polymers2,2589
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16690 Å2
ΔGint-188 kcal/mol
Surface area46440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.590, 190.090, 124.580
Angle α, β, γ (deg.)90.00, 109.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 589
2010E2 - 589
1020B10 - 241
2020F10 - 241
1030C12 - 189
2030G12 - 189
1040D15 - 467
2040H15 - 467

NCS ensembles :
ID
1
2
3
4

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Components

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NAD-reducing ... , 4 types, 8 molecules AEBFCGDH

#1: Protein NAD-reducing hydrogenase


Mass: 64214.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophilus thermoluteolus (bacteria) / References: UniProt: A0A077L6X8
#2: Protein NAD-reducing hydrogenase


Mass: 26223.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophilus thermoluteolus (bacteria) / References: UniProt: A0A077L885
#3: Protein NAD-reducing hydrogenase


Mass: 20987.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophilus thermoluteolus (bacteria) / References: UniProt: A0A077L7R5
#4: Protein NAD-reducing hydrogenase


Mass: 51926.160 Da / Num. of mol.: 2 / Fragment: UNP residues 1-468 / Source method: isolated from a natural source / Source: (natural) Hydrogenophilus thermoluteolus (bacteria) / References: UniProt: A0A077LAI5

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Non-polymers , 7 types, 786 molecules

#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#9: Chemical ChemComp-3NI / NICKEL (III) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl buffer (pH 8.5), 10% PEG 3350, 0.2 M magnesium chloride, 20 mM NAD+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.58→95.04 Å / Num. obs: 90430 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.4
Reflection shellResolution: 2.58→2.72 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2 / Num. unique obs: 13176 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→95.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.168 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24446 4487 5 %RANDOM
Rwork0.19723 ---
obs0.19957 85901 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-1.28 Å2
2--2.98 Å2-0 Å2
3----2.46 Å2
Refinement stepCycle: 1 / Resolution: 2.58→95.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22195 0 152 768 23115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01923028
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221728
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.96331317
X-RAY DIFFRACTIONr_angle_other_deg0.8623.00249675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79252866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7422.4591045
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.808153474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.79815221
X-RAY DIFFRACTIONr_chiral_restr0.0630.23486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126101
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0654.83611494
X-RAY DIFFRACTIONr_mcbond_other2.0654.83611493
X-RAY DIFFRACTIONr_mcangle_it3.4717.24614347
X-RAY DIFFRACTIONr_mcangle_other3.4717.24614348
X-RAY DIFFRACTIONr_scbond_it1.8435.05911534
X-RAY DIFFRACTIONr_scbond_other1.845.06111524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.217.5616863
X-RAY DIFFRACTIONr_long_range_B_refined5.89938.75326061
X-RAY DIFFRACTIONr_long_range_B_other5.83638.80725845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A336040.09
12E336040.09
21B134570.06
22F134570.06
31C103270.08
32G103270.08
41D286080.07
42H286080.07
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 322 -
Rwork0.29 6385 -
obs--99.97 %

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