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- PDB-5xfa: Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the H2-r... -

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Basic information

Entry
Database: PDB / ID: 5xfa
TitleCrystal structure of NAD+-reducing [NiFe]-hydrogenase in the H2-reduced state
Components(NAD-reducing ...) x 4
KeywordsOXIDOREDUCTASE / hydrogenase / Ni-Fe / Fe-S
Function / homology
Function and homology information


ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / 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. ...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. / 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 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 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, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Thioredoxin-like [2Fe-2S] ferredoxin / [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
CARBONMONOXIDE-(DICYANO) IRON / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / IRON/SULFUR CLUSTER / HoxF / HoxY / HoxU / HoxH
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)330,30524
Polymers326,7028
Non-polymers3,60316
Water2,288127
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)165,15312
Polymers163,3514
Non-polymers1,8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-195 kcal/mol
Surface area47530 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)165,15312
Polymers163,3514
Non-polymers1,8018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-189 kcal/mol
Surface area46540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.750, 192.470, 130.820
Angle α, β, γ (deg.)90.00, 105.08, 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:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLNGLNAA6 - 5836 - 583
21GLNGLNGLNGLNEE6 - 5836 - 583
12ALAALATHRTHRBB9 - 2429 - 242
22ALAALATHRTHRFF9 - 2429 - 242
13ARGARGASPASPCC12 - 18912 - 189
23ARGARGASPASPGG12 - 18912 - 189
14ASNASNTHRTHRDD18 - 46718 - 467
24ASNASNTHRTHRHH18 - 46718 - 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 , 6 types, 143 molecules

#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
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 MX300HE / Detector: CCD / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→96.24 Å / Num. obs: 86103 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 12516 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XF9

5xf9


Resolution: 2.7→96.24 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.78 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24545 4300 5 %RANDOM
Rwork0.19533 ---
obs0.19783 81782 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.064 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å20.45 Å2
2--1.41 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.7→96.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22215 0 90 127 22432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922962
X-RAY DIFFRACTIONr_bond_other_d0.0030.0221699
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9631224
X-RAY DIFFRACTIONr_angle_other_deg0.8953.00249605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5152872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9122.4621048
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.493153472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415222
X-RAY DIFFRACTIONr_chiral_restr0.0730.23479
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02126104
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025502
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_it3.9286.46311509
X-RAY DIFFRACTIONr_mcbond_other3.9286.46311508
X-RAY DIFFRACTIONr_mcangle_it6.079.68914368
X-RAY DIFFRACTIONr_mcangle_other6.079.68914369
X-RAY DIFFRACTIONr_scbond_it3.7096.811453
X-RAY DIFFRACTIONr_scbond_other3.7026.80111443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.91610.11816748
X-RAY DIFFRACTIONr_long_range_B_refined8.87851.6625411
X-RAY DIFFRACTIONr_long_range_B_other8.80651.66225399
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)
11A340530.07
12E340530.07
21B137950.04
22F137950.04
31C106940.05
32G106940.05
41D294650.05
42H294650.05
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 301 -
Rwork0.339 6012 -
obs--98.84 %

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