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- PDB-5a4m: Mechanism of Hydrogen activation by NiFe-hydrogenases -

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Basic information

Entry
Database: PDB / ID: 5a4m
TitleMechanism of Hydrogen activation by NiFe-hydrogenases
Components(HYDROGENASE-1 ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGEN ACTIVATION / NIFE HYDROGENASE / FES CLUSTERS / CATALYSIS / TRANSMEMBRANE DOMAIN
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 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 / metal ion binding / membrane
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / : / [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 1. / 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 / : / [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 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEvans, R.M. / Brooke, E.J. / Wehlin, S.A.M. / Nomerotskaia, E. / Sergent, F. / Carr, S.B. / Philips, S.E.V. / Armstrong, F.A.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Mechanism of Hydrogen Activation by [Nife] Hydrogenases.
Authors: Evans, R.M. / Brooke, E.J. / Wehlin, S.A. / Nomerotskaia, E. / Sargent, F. / Carr, S.B. / Phillips, S.E. / Armstrong, F.A.
History
DepositionJun 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HYDROGENASE-1 LARGE CHAIN
M: HYDROGENASE-1 LARGE CHAIN
S: HYDROGENASE-1 SMALL CHAIN
T: HYDROGENASE-1 SMALL CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,80016
Polymers191,3254
Non-polymers2,47512
Water26,8781492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23810 Å2
ΔGint-281.2 kcal/mol
Surface area46100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.671, 97.162, 182.911
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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HYDROGENASE-1 ... , 2 types, 4 molecules LMST

#1: Protein HYDROGENASE-1 LARGE CHAIN / HYD1 / MEMBRANE-BOUND HYDROGENASE 1 LARGE SUBUNIT / NIFE HYDROGENASE


Mass: 64751.387 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 46-311 / Source method: isolated from a natural source
Source: (natural) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
References: UniProt: P0ACD8, hydrogenase (acceptor)
#2: Protein HYDROGENASE-1 SMALL CHAIN / HYD1 / MEMBRANE-BOUND HYDROGENASE 1 SMALL SUBUNIT / NIFE HYDROGENASE


Mass: 30911.234 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-582 / Source method: isolated from a natural source
Source: (natural) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
References: UniProt: P69739, hydrogenase (acceptor)

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Non-polymers , 7 types, 1504 molecules

#3: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1492 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTRANSMEMBRANE DOMAIN DELETED

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growpH: 7.2 / Details: 0.2 M NA/K TARTRATE, 20% (W/V) PEG 3350, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→46.9 Å / Num. obs: 181455 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3USC

3usc


Resolution: 1.7→91.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.862 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.16235 8979 4.9 %RANDOM
Rwork0.13425 ---
obs0.13564 172419 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--1.32 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→91.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13133 0 66 1492 14691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01913749
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212762
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.94618715
X-RAY DIFFRACTIONr_angle_other_deg1.5853.00129361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10551733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90423.934633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.526152176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431590
X-RAY DIFFRACTIONr_chiral_restr0.1750.22005
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02115719
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023235
X-RAY DIFFRACTIONr_nbd_refined0.2780.29730
X-RAY DIFFRACTIONr_nbd_other0.2320.225298
X-RAY DIFFRACTIONr_nbtor_refined0.1860.213788
X-RAY DIFFRACTIONr_nbtor_other0.0990.213044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2680
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2620.222
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.289
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.6446800
X-RAY DIFFRACTIONr_mcbond_other1.0581.6446799
X-RAY DIFFRACTIONr_mcangle_it1.5472.4618508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0941.8866949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1352.76510140
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 627 -
Rwork0.26 12544 -
obs--98.07 %
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)
10.07950.04450.04110.05750.03620.2109-0.0139-0.00950.0167-0.00330.0062-0.007-0.0101-0.03640.00770.02150.0041-0.00680.014-0.00720.0138-16.1669.71318.191
20.11040.035-0.01260.06970.00490.227-0.0177-0.025-0.00380.00760.0042-0.02250.05670.04340.01340.02030.0131-0.00280.01880.00260.01190.765-5.45725.733
30.0858-0.047-0.03960.0552-0.03560.2117-0.01240.0077-0.0115-0.01820.0019-0.00350.0562-0.03720.01050.0363-0.00290.01010.0146-0.00510.0132-14.868-8.791-19.669
40.1017-0.04610.00380.06230.0160.2139-0.00910.01550.0073-0.0237-0.0045-0.0183-0.02410.02270.01370.02370.00050.01040.01840.00460.0092-1.4439.448-27.442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S5 - 265
2X-RAY DIFFRACTION2L2 - 582
3X-RAY DIFFRACTION3T5 - 265
4X-RAY DIFFRACTION4M2 - 582

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