[English] 日本語
Yorodumi
- PDB-2frv: CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2frv
TitleCRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Components(PERIPLASMIC HYDROGENASE) x 2
KeywordsOXIDOREDUCTASE / NI-FE HYDROGENASE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / 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 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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 / OXYGEN ATOM / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsVolbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
Citation
Journal: J.Am.Chem.Soc. / Year: 1996
Title: Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands
Authors: Volbeda, A. / Garcin, E. / Piras, C. / De Lacey, A.L. / Fernandez, V.M. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Gas Access to the Active Site of Ni-Fe Hydrogenases Probed by X-Ray Crystallography and Molecular Dynamics
Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C.
#2: Journal: Nature / Year: 1995
Title: Crystal Structure of the Nickel-Iron Hydrogenase from Desulfovibrio Gigas
Authors: Volbeda, A. / Charon, M.H. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionJun 10, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.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.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: PERIPLASMIC HYDROGENASE
L: PERIPLASMIC HYDROGENASE
A: PERIPLASMIC HYDROGENASE
B: PERIPLASMIC HYDROGENASE
C: PERIPLASMIC HYDROGENASE
D: PERIPLASMIC HYDROGENASE
E: PERIPLASMIC HYDROGENASE
F: PERIPLASMIC HYDROGENASE
G: PERIPLASMIC HYDROGENASE
H: PERIPLASMIC HYDROGENASE
I: PERIPLASMIC HYDROGENASE
J: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)534,94454
Polymers527,54012
Non-polymers7,40442
Water20,6451146
1
S: PERIPLASMIC HYDROGENASE
L: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-119 kcal/mol
Surface area24790 Å2
MethodPISA
2
A: PERIPLASMIC HYDROGENASE
B: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-119 kcal/mol
Surface area24790 Å2
MethodPISA
3
C: PERIPLASMIC HYDROGENASE
D: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-119 kcal/mol
Surface area24790 Å2
MethodPISA
4
E: PERIPLASMIC HYDROGENASE
F: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-120 kcal/mol
Surface area24800 Å2
MethodPISA
5
G: PERIPLASMIC HYDROGENASE
H: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-120 kcal/mol
Surface area24800 Å2
MethodPISA
6
I: PERIPLASMIC HYDROGENASE
J: PERIPLASMIC HYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1579
Polymers87,9232
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-120 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.780, 113.160, 133.910
Angle α, β, γ (deg.)90.03, 90.02, 119.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.495592, 0.868554, -0.001478), (-0.868525, 0.495588, 0.007514), (0.007259, -0.00244, 0.999971)-55.522, 5.831, -111.87
2given(0.501211, -0.865325, 0.000696), (0.865316, 0.501202, -0.004975), (0.003956, 0.003096, 0.999987)33.273, 45.801, -22.559
3given(-0.501305, 0.86527, -0.000384), (-0.865263, -0.501299, 0.004419), (0.003631, 0.002548, 0.99999)34.788, 57.84, -89.498
4given(-0.49544, -0.868641, 0.00131), (0.868607, -0.495433, -0.008189), (0.007763, -0.002919, 0.999965)67.429, -0.194, -44.863
5given(-1, 4.4E-5, -0.000309), (-4.3E-5, -1, -0.000306), (-0.000309, -0.000306, 1)68.106, 103.557, -66.919
DetailsTHERE ARE SIX MOLECULES PER (TRICLINIC) UNIT CELL. EACH OF THESE CONSISTS OF ONE SMALL AND ONE LARGE SUBUNIT. IN ALL STAGES THE SIX HYDROGENASE MOLECULES WERE CONSTRAINED TO OBEY EXACT NON-CRYSTALLOGRAPHIC SYMMETRY.

-
Components

-
Protein , 2 types, 12 molecules SACEGILBDFHJ

#1: Protein
PERIPLASMIC HYDROGENASE / CYTOCHROME-C3 HYDROGENASE


Mass: 28351.396 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / Cellular location: PERIPLASM / References: UniProt: P12943, 1.18.99.1
#2: Protein
PERIPLASMIC HYDROGENASE / CYTOCHROME-C3 HYDROGENASE


Mass: 59571.938 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / Cellular location: PERIPLASM / References: UniProt: P12944, 1.18.99.1

-
Non-polymers , 7 types, 1188 molecules

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


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3FeN2O
#8: Chemical
ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1146 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsTHE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY ...THE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY ANOMALOUS DIFFERENCE MAPS USING DATA COLLECTED AT BEAM LINE BM14 OF THE ESRF CLOSE TO BOTH SIDES OF THE FE ABSORPTION EDGE. THE FE HAS 3 DIATOMIC NON-PROTEIN LIGANDS (L) WHICH ARE NOW TENTATIVELY ASSIGNED TO TWO CYANIDES (BASED ON POSSIBLE HYDROGEN BONDING INTERACTIONS) AND ONE CARBON MONOXIDE (WHICH SHOWS ONLY VAN DER WAALS INTERACTIONS) (SEE ALSO HAPPE ET AL., NATURE 385, P. 126, 1997). IN ADDITION AN OXYGEN ATOM IS MODELLED IN THE ACTIVE SITE OCCUPYING A BRIDGING POSITION BETWEEN THE NI AND THE FE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growpH: 6.6 / Details: pH 6.6
Crystal grow
*PLUS
Method: unknown

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.905
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.54→29.36 Å / Num. obs: 174383 / % possible obs: 92.5 % / Observed criterion σ(I): 4 / Redundancy: 1.7 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.5
Reflection shellResolution: 2.54→2.84 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4 / % possible all: 87.4
Reflection
*PLUS
Num. measured all: 296283
Reflection shell
*PLUS
% possible obs: 87.4 %

-
Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
PROLSQrefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRV, MOLECULE 1

1frv


Resolution: 2.54→8 Å / Cross valid method: R-FREE / σ(F): 0 / Details: BEFORE PROLSQ: AMORE + X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.219 8434 5 %RANDOM
Rwork0.201 ---
all0.225 174383 --
obs0.202 168740 92.5 %-
Displacement parametersBiso mean: 9.2 Å2
Refine analyzeLuzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.54→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 223 192 6756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.015
X-RAY DIFFRACTIONp_angle_d0.0440.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.161
X-RAY DIFFRACTIONp_mcangle_it1.932
X-RAY DIFFRACTIONp_scbond_it1.991.5
X-RAY DIFFRACTIONp_scangle_it3.052.5
X-RAY DIFFRACTIONp_plane_restr0.0140.015
X-RAY DIFFRACTIONp_chiral_restr0.1690.1
X-RAY DIFFRACTIONp_singtor_nbd0.2030.35
X-RAY DIFFRACTIONp_multtor_nbd0.2080.35
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1810.35
X-RAY DIFFRACTIONp_planar_tor2.62.5
X-RAY DIFFRACTIONp_staggered_tor21.320
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.530
X-RAY DIFFRACTIONp_special_tor

+
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