[English] 日本語
Yorodumi
- PDB-1u8v: Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u8v
TitleCrystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin
ComponentsGamma-aminobutyrate metabolism dehydratase/isomerase
KeywordsLYASE / ISOMERASE / alfa-helixes / beta-strands
Function / homology
Function and homology information


4-hydroxybutanoyl-CoA dehydratase / 4-hydroxybutanoyl-CoA dehydratase activity / vinylacetyl-CoA Delta-isomerase / vinylacetyl-CoA delta-isomerase activity / oxidoreductase activity, acting on the CH-CH group of donors / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 ...4-hydroxybutyryl-coa dehydratase, domain 1 / 4-hydroxybutyryl-coa dehydratase, domain 1 / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase
Similarity search - Component
Biological speciesClostridium aminobutyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMartins, B.M. / Dobbek, H. / Cinkaya, I. / Buckel, W. / Messerschmidt, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin.
Authors: Martins, B.M. / Dobbek, H. / Cinkaya, I. / Buckel, W. / Messerschmidt, A.
History
DepositionAug 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to the authors the final electron density maps clearly indicated that Gly167 and ...SEQUENCE According to the authors the final electron density maps clearly indicated that Gly167 and Asp357 were wrongly assigned in the SWS entry. The electron density was clear for Asp at position 167 and for GLY at position 357.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyrate metabolism dehydratase/isomerase
B: Gamma-aminobutyrate metabolism dehydratase/isomerase
C: Gamma-aminobutyrate metabolism dehydratase/isomerase
D: Gamma-aminobutyrate metabolism dehydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,83712
Polymers218,2894
Non-polymers4,5498
Water42,0832336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32450 Å2
ΔGint-242 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.300, 130.200, 175.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Gamma-aminobutyrate metabolism dehydratase/isomerase


Mass: 54572.137 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Clostridium aminobutyricum (bacteria)
References: UniProt: P55792, Lyases; Carbon-oxygen lyases, vinylacetyl-CoA Delta-isomerase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2336 / 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: 2.25 Å3/Da / Density % sol: 45 %
Description: The number of unique observed reflections 563317 for the data collection and refinement refers to unmerged Friedel pairs. The value 296112 from the structure factor file refers to merged pairs.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, lithium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90004,1.73652,1.74314
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: Element LN2 cooled fixed-exit, Si(111) monochromator, Dynamically bendable mirror
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.900041
21.736521
31.743141
ReflectionResolution: 1.6→58 Å / Num. obs: 563317 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rsym value: 0.045 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.164 / % possible all: 96.4

-
Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
SnBphasing
SHARPphasing
SHELXrefinement
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→58 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used.
RfactorNum. reflectionSelection details
Rfree0.212 8769 random
Rwork0.163 --
obs0.165 563317 -
Refinement stepCycle: LAST / Resolution: 1.6→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15244 0 244 2336 17824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.75

+
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