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- PDB-3usc: Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxid... -

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Basic information

Entry
Database: PDB / ID: 3usc
TitleCrystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / MEMBRANE-BOUND HYDROGENASE
Function / homology
Function and homology information


hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / anaerobic respiration / ferredoxin hydrogenase activity ...hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / 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
NICKEL (III) ION / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / : / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C. / Darnault, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Authors: Volbeda, A. / Amara, P. / Darnault, C. / Mouesca, J.M. / Parkin, A. / Roessler, M.M. / Armstrong, F.A. / Fontecilla-Camps, J.C.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ptnr1_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,09428
Polymers203,1324
Non-polymers3,96124
Water22,1941232
1
S: Hydrogenase-1 small chain
L: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,43613
Polymers101,5662
Non-polymers1,87011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-158 kcal/mol
Surface area26250 Å2
MethodPISA
2
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,65715
Polymers101,5662
Non-polymers2,09113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-176 kcal/mol
Surface area26260 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27040 Å2
ΔGint-367 kcal/mol
Surface area47260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.170, 98.160, 183.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
12S
22T
13L
23M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111S5 - 92
2111T5 - 92
1213S93
2213T93
1311S94 - 100
2311T94 - 100
1413S101
2413T101
1511S102 - 124
2511T102 - 124
1613S125
2613T125
1711S126 - 173
2711T126 - 173
1813S174 - 175
2813T174 - 175
1911S343 - 404
2911T343 - 404
1121S176 - 202
2121T176 - 202
1223S203
2223T203
1321S204 - 269
2321T204 - 269
1421S341 - 402
2421T341 - 402
1131L2 - 5
2131M2 - 5
1233L6
2233M6
1331L7 - 39
2331M7 - 39
1433L40
2433M40
1531L41 - 97
2531M41 - 97
1633L98
2633M98
1731L99 - 134
2731M99 - 134
1833L135
2833M135
1931L136 - 138
2931M136 - 138
11033L139
21033M139
11131L140
21131M140
11233L141 - 143
21233M141 - 143
11331L144 - 170
21331M144 - 170
11433L171 - 175
21433M171 - 175
11531L176 - 316
21531M176 - 316
11633L317
21633M317
11731L318 - 331
21731M318 - 331
11833L332 - 333
21833M332 - 333
11931L334 - 379
21931M334 - 379
12033L380
22033M380
12131L381 - 382
22131M381 - 382
12233L383 - 387
22233M383 - 387
12331L388 - 423
22331M388 - 423
12436L424 - 433
22436M424 - 433
12531L434 - 487
22531M434 - 487
12633L488 - 489
22633M488 - 489
12731L490 - 518
22731M490 - 518
12833L519
22833M519
12931L520 - 702
22931M520 - 703

NCS ensembles :
ID
1
2
3
DetailsTHE TWO DESCRIBED BIOMOLECULES 1 AND 2 ARE RELATED BY NON-CRYSTALLOGRAPHIC TWOFOLD SYMMETRY. IT IS PLAUSIBLE THAT TOGETHER THEY FORM A FUNCTIONAL TETRAMER (WHICH MAY ALSO BE DESCRIBED AS A DIMER OF HETERO-DIMERS, BIOMOLECULE 3).

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Components

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Hydrogenase-1 ... , 2 types, 4 molecules STLM

#1: Protein Hydrogenase-1 small chain


Mass: 36814.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: b0972, hyaA, JW0954 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain


Mass: 64751.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC4100 / Gene: b0973, hyaB, JW0955 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Sugars , 1 types, 2 molecules

#6: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 1254 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.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1232 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSF3 DESIGNATES A FE4-S3 CLUSTER IN A VERY OXIDIZED STATE WITH TOTAL CORE CHARGE OF +5 RELATIONSHIP ...SF3 DESIGNATES A FE4-S3 CLUSTER IN A VERY OXIDIZED STATE WITH TOTAL CORE CHARGE OF +5 RELATIONSHIP BETWEEN ATOMS IN SF3 AND F4S (REDUCED FORM OF THE FE4-S3 CLUSTER WITH TOTAL CORE CHARGE OF +4 OR +3): FS4 ATOMS FE1, FE2, FE3, FE4, S1, S2 AND S3 CORRESPOND TO SF3 ATOMS FE4, FE1, FE3, FE7, S2, S3 AND S1, RESPECTIVELY

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: PEG4000, LiSO4, ferricyanide, OH-NQ, pH 5.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 5, 2011 / Details: focusing mirrors
RadiationMonochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 189394 / Num. obs: 101239 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.893 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.10.3693.86926025600184.6
2.1-2.240.2745.048019128997185.6
2.24-2.410.2166.527519426751185.8
2.41-2.640.1628.437586026304186.4
2.64-2.930.12111.046585022368186
2.93-3.380.08115.386343421101185.6
3.38-4.120.05122.345231017384184.2
4.12-5.80.03529.964213413574183.2
5.8-200.02638.03231407156180.3
20-300.0243.44396123175.9
30-1000.02339.39236157.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of as-isolated hydrogenase-1 refined at 1.67A resolution

Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1556 / WRfactor Rwork: 0.126 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9146 / SU B: 6.711 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1915 / SU Rfree: 0.1482 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement, + tight NCS restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 5076 5 %RANDOM
Rwork0.1406 ---
all0.1424 101213 --
obs0.1424 101213 87.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 45.92 Å2 / Biso mean: 11.328 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2--0.72 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13182 0 116 1232 14530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214107
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9519252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74951819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96223.861663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.771152288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.815101
X-RAY DIFFRACTIONr_chiral_restr0.0870.22054
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110971
X-RAY DIFFRACTIONr_mcbond_it1.0671.58636
X-RAY DIFFRACTIONr_mcangle_it1.6952.513991
X-RAY DIFFRACTIONr_scbond_it2.735471
X-RAY DIFFRACTIONr_scangle_it4.09155168
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1S1295TIGHT POSITIONAL0.10.2
1S15LOOSE POSITIONAL12
1S1295TIGHT THERMAL0.411
1S15LOOSE THERMAL0.4710
2S762TIGHT POSITIONAL0.130.2
2S5LOOSE POSITIONAL0.12
2S762TIGHT THERMAL0.421
2S5LOOSE THERMAL0.4910
3L4281TIGHT POSITIONAL0.080.2
3L173LOOSE POSITIONAL0.722
3L4281TIGHT THERMAL0.421
3L173LOOSE THERMAL0.4710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 372 -
Rwork0.179 7101 -
all-7473 -
obs-7101 89.09 %
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)
10.27790.0584-0.1130.13670.04680.7717-0.03020.0294-0.0802-0.01560.0022-0.01010.1027-0.01360.0280.0422-0.00970.01050.0052-0.00840.0541-10.897-16.1895-22.8383
20.4525-0.0713-0.01210.3884-0.27850.78430.00350.01490.00930.01770.0090.0475-0.0354-0.2002-0.01250.0110.00770.00310.0646-0.00360.0255-26.95522.8366-10.034
30.2869-0.0712-0.00990.24290.02740.499-0.00140.03630.0146-0.0270.0034-0.0649-0.06450.0748-0.00190.0223-0.01730.00610.02040.00240.04020.53555.7757-26.0635
40.2324-0.04670.05710.15780.04380.8734-0.0213-0.04130.08930.0272-0.0071-0.0293-0.13210.02360.02840.0716-0.0064-0.01430.0108-0.01360.0729-8.539613.912424.4723
50.36390.0420.07060.5654-0.10090.5728-0.0065-0.00870.02790.00230.01320.0884-0.0382-0.166-0.00670.01190.009-0.0010.0499-0.00150.0255-27.6829-1.667111.2885
60.34580.07550.04120.20780.03110.48380.0003-0.0436-0.00950.0379-0.0067-0.05460.04050.07460.00640.01950.0086-0.01130.01930.00330.0337-1.507-9.684627.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S4 - 175
2X-RAY DIFFRACTION1S403 - 404
3X-RAY DIFFRACTION2S176 - 268
4X-RAY DIFFRACTION2S401 - 402
5X-RAY DIFFRACTION3L2 - 582
6X-RAY DIFFRACTION3L601 - 603
7X-RAY DIFFRACTION3L701 - 705
8X-RAY DIFFRACTION4T4 - 175
9X-RAY DIFFRACTION4T403 - 404
10X-RAY DIFFRACTION5T176 - 268
11X-RAY DIFFRACTION5T401 - 402
12X-RAY DIFFRACTION6M2 - 582
13X-RAY DIFFRACTION6M601 - 603
14X-RAY DIFFRACTION6M702 - 706

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