[English] 日本語
Yorodumi
- PDB-2yiv: NI,FE-CODH with n-butylisocyanate state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yiv
TitleNI,FE-CODH with n-butylisocyanate state
ComponentsCARBON MONOXIDE DEHYDROGENASE 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / N-BUTYL ISOCYANIDE / IRON/SULFUR CLUSTER / FE(3)-NI(1)-S(4) CLUSTER / N-butylformamide / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsJeoung, J.H. / Dobbek, H.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2012
Title: N-Butyl Isocyanide Oxidation at the [Nife4S4Oh(X)] Cluster of Co Dehydrogenase.
Authors: Jeoung, J.H. / Dobbek, H.
History
DepositionMay 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Atomic model / Derived calculations / Other
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3147
Polymers69,1921
Non-polymers1,1226
Water14,880826
1
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules

X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,62814
Polymers138,3842
Non-polymers2,24412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8510 Å2
ΔGint-78.1 kcal/mol
Surface area38340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.700, 75.240, 71.220
Angle α, β, γ (deg.)90.00, 111.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2110-

HOH

21X-2142-

HOH

31X-2400-

HOH

41X-2467-

HOH

-
Components

-
Protein , 1 types, 1 molecules X

#1: Protein CARBON MONOXIDE DEHYDROGENASE 2 / / CODH 2


Mass: 69191.891 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2091 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q9F8A8, carbon-monoxide dehydrogenase (acceptor)

-
Non-polymers , 7 types, 832 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-WCC / FE(3)-NI(1)-S(4) CLUSTER / C CLUSTER CUBANE


Mass: 354.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3NiS4
#5: Chemical ChemComp-YIV / N-butylformamide


Mass: 101.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO
#6: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-NBN / N-BUTYL ISOCYANIDE


Mass: 83.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN X, LYS 3 TO ARG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.46 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.28→20 Å / Num. obs: 138376 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.57
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.64 / % possible all: 82.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B53

3b53


Resolution: 1.28→18.9 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 13.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1433 6919 5 %
Rwork0.1123 --
obs0.1139 138367 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.735 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4499 Å20 Å2-1.7723 Å2
2---1.4271 Å20 Å2
3----0.0228 Å2
Refinement stepCycle: LAST / Resolution: 1.28→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 34 826 5530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155172
X-RAY DIFFRACTIONf_angle_d1.9767158
X-RAY DIFFRACTIONf_dihedral_angle_d12.1841985
X-RAY DIFFRACTIONf_chiral_restr0.175846
X-RAY DIFFRACTIONf_plane_restr0.006927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.32570.24876200.183711785X-RAY DIFFRACTION88
1.3257-1.37880.19926870.148613044X-RAY DIFFRACTION97
1.3788-1.44150.1786960.126613225X-RAY DIFFRACTION98
1.4415-1.51750.15346940.105713177X-RAY DIFFRACTION98
1.5175-1.61250.14616970.094913243X-RAY DIFFRACTION98
1.6125-1.7370.13546990.091313300X-RAY DIFFRACTION99
1.737-1.91160.12687030.088713340X-RAY DIFFRACTION99
1.9116-2.18790.1317040.095813374X-RAY DIFFRACTION99
2.1879-2.75510.12597080.099913463X-RAY DIFFRACTION99
2.7551-18.90170.12777110.118613497X-RAY DIFFRACTION99

+
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