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- PDB-3myr: Crystal structure of [NiFe] hydrogenase from Allochromatium vinos... -

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Basic information

Entry
Database: PDB / ID: 3myr
TitleCrystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state
Components
  • Hydrogenase (NiFe) small subunit HydA
  • Nickel-dependent hydrogenase large subunit
KeywordsOXIDOREDUCTASE / [NiFe] hydrogenase / Allochromatium vinosum / photosynthetic purple-sulfur bacterium / iron-sulfur cluster / Ni-A state
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / metal ion binding / plasma membrane
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 / IMIDAZOLE / NI-FE OXIDIZED ACTIVE CENTER / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / Hydrogenase (acceptor)
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOgata, H. / Kellers, P. / Lubitz, W.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state).
Authors: Ogata, H. / Kellers, P. / Lubitz, W.
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrogenase (NiFe) small subunit HydA
B: Nickel-dependent hydrogenase large subunit
C: Hydrogenase (NiFe) small subunit HydA
D: Nickel-dependent hydrogenase large subunit
E: Hydrogenase (NiFe) small subunit HydA
F: Nickel-dependent hydrogenase large subunit
G: Hydrogenase (NiFe) small subunit HydA
H: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,97934
Polymers364,7638
Non-polymers5,21626
Water34,6791925
1
A: Hydrogenase (NiFe) small subunit HydA
B: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5299
Polymers91,1912
Non-polymers1,3397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-101 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: Hydrogenase (NiFe) small subunit HydA
D: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4608
Polymers91,1912
Non-polymers1,2696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-101 kcal/mol
Surface area25620 Å2
MethodPISA
3
E: Hydrogenase (NiFe) small subunit HydA
F: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4608
Polymers91,1912
Non-polymers1,2696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-101 kcal/mol
Surface area25300 Å2
MethodPISA
4
G: Hydrogenase (NiFe) small subunit HydA
H: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5299
Polymers91,1912
Non-polymers1,3397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-101 kcal/mol
Surface area25540 Å2
MethodPISA
5
A: Hydrogenase (NiFe) small subunit HydA
B: Nickel-dependent hydrogenase large subunit
C: Hydrogenase (NiFe) small subunit HydA
D: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,98917
Polymers182,3824
Non-polymers2,60813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-209 kcal/mol
Surface area45320 Å2
MethodPISA
6
E: Hydrogenase (NiFe) small subunit HydA
F: Nickel-dependent hydrogenase large subunit
G: Hydrogenase (NiFe) small subunit HydA
H: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,98917
Polymers182,3824
Non-polymers2,60813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23600 Å2
ΔGint-207 kcal/mol
Surface area44930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.750, 216.960, 119.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12E
22G
13B
23D
14F
24H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA3 - 2671 - 265
21ALAALAVALVALCC3 - 2671 - 265
12ALAALAVALVALEE3 - 2671 - 265
22ALAALAVALVALGG3 - 2671 - 265
13ARGARGHISHISBB1004 - 15614 - 561
23ARGARGHISHISDD1004 - 15614 - 561
14ARGARGHISHISFF1004 - 15614 - 561
24ARGARGHISHISHH1004 - 15614 - 561

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Hydrogenase (NiFe) small subunit HydA


Mass: 29141.926 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum (bacteria) / Strain: DSM 185 / References: UniProt: D3RV29, hydrogenase (acceptor)
#2: Protein
Nickel-dependent hydrogenase large subunit


Mass: 62048.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum (bacteria) / Strain: DSM 185 / References: UniProt: D3RV26

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Non-polymers , 7 types, 1951 molecules

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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1925 / 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: 3.67 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: Imidazole, sodium citrate, pH 8.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2009 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.06 Å / Num. all: 295408 / Num. obs: 295408 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.16 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 4.22 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.9 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WUI

1wui


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.297 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16811 15482 5 %RANDOM
Rwork0.138 ---
obs0.13952 294160 100 %-
all-294160 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.902 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---1.63 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25641 0 146 1925 27712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02226639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.95736213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91653305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68323.3221216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55153970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.00815196
X-RAY DIFFRACTIONr_chiral_restr0.3390.23898
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02120682
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3551.516477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.262226436
X-RAY DIFFRACTIONr_scbond_it4.293310162
X-RAY DIFFRACTIONr_scangle_it6.5244.59669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2018MEDIUM POSITIONAL0.270.5
1A2018MEDIUM THERMAL1.82
2E2018MEDIUM POSITIONAL0.260.5
2E2018MEDIUM THERMAL1.542
3B4354MEDIUM POSITIONAL0.250.5
3B4354MEDIUM THERMAL1.722
4F4354MEDIUM POSITIONAL0.270.5
4F4354MEDIUM THERMAL1.322
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 1135 -
Rwork0.175 21552 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41890.05520.10470.41330.0190.339-0.01410.03010.0421-0.02330.01160.0374-0.0252-0.04440.00250.00450.00150.00560.0286-0.00040.0527-34.3972-5.3772-40.9644
20.41340.12190.06290.49630.03210.31490.00070.0927-0.085-0.08110.0251-0.03570.0826-0.0117-0.02570.0384-0.0080.00260.0273-0.03150.0598-31.518-28.2327-48.3914
30.45240.1053-0.00110.4544-0.12820.54920.0525-0.1113-0.06470.1322-0.066-0.1550.01930.05360.01350.0457-0.0209-0.04740.04320.0110.0842-9.0542-12.2768-9.726
40.45420.0830.05720.3955-0.05440.42910.0796-0.2198-0.02580.2378-0.0689-0.00880.0204-0.1128-0.01070.1515-0.0629-0.01170.1406-0.00110.0212-27.8155-16.68954.6123
50.5089-0.07740.19590.5692-0.13230.58480.08050.1422-0.06-0.212-0.0459-0.03320.14280.0605-0.03460.14670.0704-0.02270.0753-0.04410.0437-43.5720.0634-100.6276
60.4196-0.02610.10910.5333-0.09630.42860.04340.0588-0.005-0.1654-0.01670.1240.0469-0.1028-0.02660.08520.0366-0.06330.0739-0.02310.0892-63.544433.0742-97.6531
70.4294-0.05610.24060.3921-0.18410.44670.0222-0.0388-0.0245-0.0066-0.01640.00790.0535-0.0374-0.00580.03260.0143-0.01990.03480.00670.0573-38.218118.4645-60.3587
80.3844-0.11170.19260.4094-0.15510.4723-0.02910.01890.10560.0375-0.0491-0.1352-0.0770.07740.07820.03370.0045-0.03710.04160.01740.1153-23.20537.1302-61.5392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999

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