[English] 日本語
Yorodumi
- PDB-4ko3: Low X-ray dose structure of anaerobically purified Dm. baculatum ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ko3
TitleLow X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Components
  • Nickel-dependent hydrogenase large subunit
  • Periplasmic [NiFeSe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / NiFeSe-site / H2 cleavage/production / seleninate
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / 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
CARBONMONOXIDE-(DICYANO) IRON / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / Periplasmic [NiFeSe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfomicrobium baculatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVolbeda, A. / Cavazza, C. / Fontecilla-Camps, J.C.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2013
Title: Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase.
Authors: Volbeda, A. / Amara, P. / Iannello, M. / De Lacey, A.L. / Cavazza, C. / Fontecilla-Camps, J.C.
#1: Journal: Structure / Year: 1999
Title: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
Authors: Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionMay 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Other
Revision 1.4Apr 9, 2014Group: Other
Revision 1.5Jun 8, 2016Group: Atomic model
Revision 2.0May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_distant_solvent_atoms ...entity_poly / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Oct 26, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _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_alt_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_alt_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_alt_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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Periplasmic [NiFeSe] hydrogenase small subunit
L: Nickel-dependent hydrogenase large subunit
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,68829
Polymers172,3964
Non-polymers3,29225
Water33,2021843
1
S: Periplasmic [NiFeSe] hydrogenase small subunit
L: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,82114
Polymers86,1982
Non-polymers1,62312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-149 kcal/mol
Surface area24780 Å2
MethodPISA
2
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,86615
Polymers86,1982
Non-polymers1,66813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-157 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.200, 108.720, 136.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules STLM

#1: Protein Periplasmic [NiFeSe] hydrogenase small subunit / NiFeSe hydrogenlyase small chain


Mass: 30874.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / References: UniProt: P13063, hydrogenase (acceptor)
#2: Protein Nickel-dependent hydrogenase large subunit /


Mass: 55323.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / Strain: DSM 4028 / VKM B-1378 / References: UniProt: C7LN88, 1.18.99.1

-
Non-polymers , 8 types, 1868 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#9: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1843 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsRESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE (O=SE-O, CONFORMATION ...RESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE (O=SE-O, CONFORMATION LABELED O); SEC = NON-OXIDIZED SELENOATE (CONFORMATION R, WITH NI-SE BOND); UOX = SELENENATE (SE-O, CONFORMATION P, WITH NI-SE AND FE-O BOND). A DISULFIDE BOND BETWEEN CYS70 AND CYS73 HAS BEEN TENTATIVELY ASSIGNED TO THE PARTIALLY RESOLVED UOX-CONTAINING FRACTION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.1399 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2010
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1399 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 173572 / Num. obs: 171915 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.177 / Net I/σ(I): 6.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.65 / Num. unique all: 27085 / Rsym value: 1.349 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KL8

4kl8


Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.334 / SU ML: 0.073 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20071 8712 5.1 %RANDOM
Rwork0.16385 ---
obs0.16573 163172 99.05 %-
all-173542 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20 Å2
2---0.48 Å2-0 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.103 Å0.179 Å
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 99 1843 13886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212692
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.97717192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42124.417566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.691152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021565
X-RAY DIFFRACTIONr_chiral_restr0.0850.21902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219521
X-RAY DIFFRACTIONr_mcbond_it1.6331.57735
X-RAY DIFFRACTIONr_mcangle_it2.5222.512565
X-RAY DIFFRACTIONr_scbond_it3.66434957
X-RAY DIFFRACTIONr_scangle_it5.2554549
X-RAY DIFFRACTIONr_rigid_bond_restr1.938312692
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 581 -
Rwork0.335 10834 -
obs-11426 90.17 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more