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- PDB-4ue3: The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the... -

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Entry
Database: PDB / ID: 4ue3
TitleThe Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / MEMBRANE-BOUND HYDROGENASE / NI-FE HYDROGENASE / HYDROGEN
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
: / [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 ...: / [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 / 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
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEvans, R.M. / Wehlin, S.A.M. / 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
DepositionDec 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 2.0Dec 4, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / audit_conform / chem_comp / database_PDB_matrix / diffrn / diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_database_related / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_database_status.SG_entry / _pdbx_database_status.pdb_format_compatible / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_ligand_of_interest / _pdbx_entry_details.sequence_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_low / _reflns_shell.number_unique_obs / _software.version / _struct.pdbx_CASP_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: Modelling of the water structure, particularly around the active site cavity improved
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Nov 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
SSS: Hydrogenase-1 small chain
LLL: Hydrogenase-1 large chain
TTT: Hydrogenase-1 small chain
MMM: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,37425
Polymers187,4694
Non-polymers2,90521
Water24,1401340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25710 Å2
ΔGint-377 kcal/mol
Surface area46500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.521, 97.405, 183.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 29126.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64608.176 Da / Num. of mol.: 2 / Mutation: R509K
Source method: isolated from a genetically manipulated source
Details: Variant R509K
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Non-polymers , 10 types, 1361 molecules

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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 1340 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM Bis tris pH 5.5-5.9, 150 mM NaCl 200 mM Li2SO4 19-21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→48.75 Å / Num. obs: 317004 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12063 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3usc

3usc


Resolution: 1.4→48.75 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.148 / WRfactor Rwork: 0.128 / SU B: 0.904 / SU ML: 0.035 / Average fsc free: 0.9476 / Average fsc work: 0.9527 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1602 15658 4.941 %
Rwork0.1397 301266 -
all0.141 --
obs-316924 96.835 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.141 Å20 Å20 Å2
2---0.046 Å20 Å2
3----0.095 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13166 0 87 1340 14593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01313861
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712497
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.64318933
X-RAY DIFFRACTIONr_angle_other_deg1.6331.57429070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55851764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29422.174736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.032152219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7991593
X-RAY DIFFRACTIONr_chiral_restr0.1030.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022973
X-RAY DIFFRACTIONr_nbd_refined0.2340.23034
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.212547
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26875
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.25946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2905
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.26
X-RAY DIFFRACTIONr_nbd_other0.2140.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.236
X-RAY DIFFRACTIONr_mcbond_it1.0321.1296840
X-RAY DIFFRACTIONr_mcbond_other1.0331.136839
X-RAY DIFFRACTIONr_mcangle_it1.4641.6948565
X-RAY DIFFRACTIONr_mcangle_other1.4641.6938566
X-RAY DIFFRACTIONr_scbond_it2.1461.3437021
X-RAY DIFFRACTIONr_scbond_other2.1471.3417011
X-RAY DIFFRACTIONr_scangle_it3.1871.93310287
X-RAY DIFFRACTIONr_scangle_other3.1871.9310275
X-RAY DIFFRACTIONr_lrange_it4.01214.24816366
X-RAY DIFFRACTIONr_lrange_other3.91813.93516098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.2869220.28417603X-RAY DIFFRACTION76.9694
1.436-1.4760.25910670.25220644X-RAY DIFFRACTION92.929
1.476-1.5180.21610690.19621128X-RAY DIFFRACTION97.4065
1.518-1.5650.211080.17320571X-RAY DIFFRACTION97.9488
1.565-1.6170.18910680.15819984X-RAY DIFFRACTION98.1262
1.617-1.6730.18810210.14919464X-RAY DIFFRACTION98.3815
1.673-1.7360.169460.13618813X-RAY DIFFRACTION98.4897
1.736-1.8070.1510010.12818054X-RAY DIFFRACTION98.6948
1.807-1.8880.1499250.12417399X-RAY DIFFRACTION98.8669
1.888-1.980.1568900.12416714X-RAY DIFFRACTION99.1049
1.98-2.0870.1547950.12515953X-RAY DIFFRACTION99.1593
2.087-2.2130.1447500.12115161X-RAY DIFFRACTION99.3692
2.213-2.3660.1357180.11714262X-RAY DIFFRACTION99.5018
2.366-2.5550.1426570.11813315X-RAY DIFFRACTION99.6221
2.555-2.7990.1496110.12512327X-RAY DIFFRACTION99.7687
2.799-3.1290.1515610.13211199X-RAY DIFFRACTION99.8641
3.129-3.6120.1455300.1399907X-RAY DIFFRACTION99.9521
3.612-4.4230.144430.1238416X-RAY DIFFRACTION99.9887
4.423-6.2470.1513770.146566X-RAY DIFFRACTION99.9712
6.247-48.750.1642000.163787X-RAY DIFFRACTION99.2038

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