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- PDB-5adu: The Mechanism of Hydrogen Activation by NiFe-hydrogenases -

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Basic information

Entry
Database: PDB / ID: 5adu
TitleThe Mechanism of Hydrogen Activation by NiFe-hydrogenases
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / NIFE-HYDROGENASE / HYDROGEN LYSIS
Function / homology
Function and homology information


hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity ...hydrogen metabolic process / [Ni-Fe] hydrogenase complex / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / 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
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / 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: 1.1 Å
AuthorsEvans, R. / Brooke, E.J. / Wehlin, S.A. / Nomerotskaia, E. / Sargent, F. / Carr, S.B. / Phillips, 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
DepositionAug 24, 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 1.3Nov 14, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / struct_ref
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Jan 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_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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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)206,88724
Polymers203,1604
Non-polymers3,72720
Water19,6901093
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26640 Å2
ΔGint-333.8 kcal/mol
Surface area48400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.855, 98.979, 185.207
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: 64765.418 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 46-372 / Mutation: D118N,D574N
Source method: isolated from a genetically manipulated source
Details: DOUBLE MUTANT PROTEIN
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 36814.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P69739, hydrogenase (acceptor)

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Sugars , 1 types, 2 molecules

#10: 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 , 9 types, 1111 molecules

#3: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1093 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPOINT MUTATIONS D118N AND D574N ADDED TO INVESTIGATE THE EFFECT ON CATALYSIS

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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: 2.14 Å3/Da / Density % sol: 42.7 %
Description: DATA WERE COLLECTED AS A LINE SCAN TO MINIMISE RADIATION DAMAGE.
Crystal growpH: 6
Details: 100 MM BIS-TRIS PH 6.0, 21 % PEG 3350, 200 MM LISO4, 150 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.1→49.5 Å / Num. obs: 665775 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.5
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.7 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3USC

3usc


Resolution: 1.1→92.78 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.884 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14238 33298 5 %RANDOM
Rwork0.12612 ---
obs0.12693 632387 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.686 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.1→92.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13163 0 104 1093 14360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914080
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213154
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.94519243
X-RAY DIFFRACTIONr_angle_other_deg1.073330353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11251821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31723.879660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.911152284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.30215100
X-RAY DIFFRACTIONr_chiral_restr0.1070.22045
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116190
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023338
X-RAY DIFFRACTIONr_nbd_refined0.2290.27510
X-RAY DIFFRACTIONr_nbd_other0.1520.222708
X-RAY DIFFRACTIONr_nbtor_refined0.1640.212696
X-RAY DIFFRACTIONr_nbtor_other0.070.210672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2430.26
X-RAY DIFFRACTIONr_metal_ion_refined0.2380.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1390.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8290.866905
X-RAY DIFFRACTIONr_mcbond_other0.8290.866904
X-RAY DIFFRACTIONr_mcangle_it1.0541.3028662
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4031.1037175
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6621.5710472
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.03527234
X-RAY DIFFRACTIONr_sphericity_free18.2645343
X-RAY DIFFRACTIONr_sphericity_bonded5.27527568
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 2338 -
Rwork0.269 44980 -
obs--92.08 %

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