[English] 日本語
Yorodumi
- PDB-1ffv: CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ffv
TitleCARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA
Components
  • CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
  • CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
KeywordsHYDROLASE / DEHYDROGENASE
Function / homology
Function and homology information


aerobic carbon monoxide dehydrogenase / carbon-monoxide oxygenase activity / anaerobic carbon-monoxide dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / metal ion binding
Similarity search - Function
Carbon-monoxide dehydrogenase, large subunit / : / : / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Carbon-monoxide dehydrogenase, large subunit / : / : / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-PCD / : / Carbon monoxide dehydrogenase large chain / Carbon monoxide dehydrogenase medium chain / Carbon monoxide dehydrogenase small chain
Similarity search - Component
Biological speciesHydrogenophaga pseudoflava (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsHaenzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.
Authors: Hanzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
A: CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
B: CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
C: CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
D: CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
E: CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
F: CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,25314
Polymers271,2906
Non-polymers3,9638
Water28,9501607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28810 Å2
ΔGint-195 kcal/mol
Surface area76340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.373, 193.793, 218.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 17747.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19915
#2: Protein CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 87345.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: GenBank: 4098682, UniProt: P19913*PLUS
#3: Protein CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE


Mass: 30552.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19914

-
Non-polymers , 4 types, 1615 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-PCD / (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / MOLYBDENUM COFACTOR / MOCO


Mass: 844.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26MoN8O16P2S2
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1607 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: potassium sodium tartrate, dihydrogen ammonium phosphate, methylpentandediol, dithioerythritol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135.5 mg/mlprotein1drop
250 mMHEPES-NaOH1drop
31.1 Msodium potassium tartrate1reservoir
40.3 Mammonium phosphate1reservoir
53 %(w/v)MPD1reservoir
610 mMDTE1reservoir

-
Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 433970 / Num. obs: 407833 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.7
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.358 / Num. unique all: 165339 / % possible all: 79.7
Reflection
*PLUS
Num. obs: 162740 / Num. measured all: 433970
Reflection shell
*PLUS
% possible obs: 79.7 %

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
RefinementResolution: 2.25→20 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.237 8090 Random
Rwork0.209 --
all-165339 -
obs-154650 -
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22926 0 218 4821 27965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.72
X-RAY DIFFRACTIONc_angle_deg0.0073
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.72
LS refinement shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.32 Å / Rfactor Rfree: 0.341 / Rfactor obs: 0.323

+
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