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- PDB-6gal: Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q colle... -

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Basic information

Entry
Database: PDB / ID: 6gal
TitleStructure of fully reduced Hydrogenase (Hyd-1) variant E28Q collected at pH 10
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / NiFe hydrogenase / Iron sulphur cluster / periplasm / 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
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
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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 / pdbx_struct_conn_angle / refine / struct_conn
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _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.ptnr1_symmetry / _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_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)206,00221
Polymers203,1304
Non-polymers2,87217
Water24,8611380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25010 Å2
ΔGint-296 kcal/mol
Surface area46380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.906, 95.224, 183.910
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: 36814.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Two additional amino acids visible at N-terminus relative to chain S
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Description: chromosomal copy of the HybA gene has been engineered to add a his-tag
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: 64750.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Variant E28Q / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Non-polymers , 10 types, 1397 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.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#11: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1380 / 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: 2.08 Å3/Da / Density % sol: 40.8 % / Description: Long rods with rectangular cross section
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 100 mM tris pH 8.1, 200 mm LiSO4 150 mM NaCl 19-21% PEG 3350
PH range: 8.0-8.2 / Temp details: Ambient temperature in anaerobic glove box

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.25→95 Å / Num. obs: 437084 / % possible obs: 95.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.5
Reflection shellResolution: 1.25→1.32 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LMM

5lmm


Resolution: 1.25→92.12 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.386 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.147 22000 5 %RANDOM
Rwork0.12 ---
obs0.121 414972 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.25→92.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13181 0 90 1380 14651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01913905
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212532
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.94218982
X-RAY DIFFRACTIONr_angle_other_deg1.153329142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04951768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33723.906640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.053152219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571593
X-RAY DIFFRACTIONr_chiral_restr0.1440.22022
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02115664
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022893
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_it0.9880.9286880
X-RAY DIFFRACTIONr_mcbond_other0.9880.9286879
X-RAY DIFFRACTIONr_mcangle_it1.2151.4018628
X-RAY DIFFRACTIONr_mcangle_other1.2151.4018629
X-RAY DIFFRACTIONr_scbond_it1.7251.167025
X-RAY DIFFRACTIONr_scbond_other1.7191.1587022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0341.65110277
X-RAY DIFFRACTIONr_long_range_B_refined2.33412.29616375
X-RAY DIFFRACTIONr_long_range_B_other2.11211.92116099
X-RAY DIFFRACTIONr_rigid_bond_restr2.593326435
X-RAY DIFFRACTIONr_sphericity_free19.9725931
X-RAY DIFFRACTIONr_sphericity_bonded5.915526488
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 1555 -
Rwork0.221 29504 -
obs--92.53 %

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