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- PDB-6fpi: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q -

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Basic information

Entry
Database: PDB / ID: 6fpi
TitleStructure of fully reduced Hydrogenase (Hyd-1) variant E28Q
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / NiFe hydrogenase / Iron sulphur cluster / periplasm / hydrogen
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B ...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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / 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
NI-FE REDUCED ACTIVE CENTER / FE3-S4 CLUSTER / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarr, S.B. / Armstrong, F.A. / Evans, R.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N006321/1 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.
Authors: Evans, R.M. / Ash, P.A. / Beaton, S.E. / Brooke, E.J. / Vincent, K.A. / Carr, S.B. / Armstrong, F.A.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.value
Revision 2.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)204,68823
Polymers200,9844
Non-polymers3,70419
Water22,0861226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25690 Å2
ΔGint-328 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.820, 97.730, 183.200
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 STLM

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


Mass: 35741.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: RME018 / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64750.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Variant E28Q / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: RME018 / 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 , 8 types, 1243 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
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EJ2 / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#9: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.46 % / Description: Rods with rectangular cross-section
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 100 mM Bis-tris pH 5.5-5.9, 200 mM LiSO4, 150 mM NaCl 19-22% PEG 3350
PH range: 5.5-5.9 / Temp details: Ambient temperature in anaerobic chamber

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.5→83.51 Å / Num. obs: 263161 / % possible obs: 98.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.57 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LMM

5lmm


Resolution: 1.5→83.51 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.657 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 13349 5.1 %RANDOM
Rwork0.145 ---
obs0.146 249661 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--1.56 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→83.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13225 0 101 1226 14552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01914006
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212667
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.94319120
X-RAY DIFFRACTIONr_angle_other_deg1.05329472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98651787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.423.92653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.372152241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8421596
X-RAY DIFFRACTIONr_chiral_restr0.1120.22036
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02115755
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022909
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_it1.4431.9346897
X-RAY DIFFRACTIONr_mcbond_other1.4431.9346896
X-RAY DIFFRACTIONr_mcangle_it1.9722.8938641
X-RAY DIFFRACTIONr_mcangle_other1.9722.8938642
X-RAY DIFFRACTIONr_scbond_it2.5532.2347109
X-RAY DIFFRACTIONr_scbond_other2.5532.2357108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9243.23810393
X-RAY DIFFRACTIONr_long_range_B_refined5.11824.14516352
X-RAY DIFFRACTIONr_long_range_B_other4.9823.71616094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 926 -
Rwork0.299 18118 -
obs--96.54 %

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