[English] 日本語
Yorodumi
- PDB-5z7r: Crystal structure of crotonase from Clostridium acetobutylicum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z7r
TitleCrystal structure of crotonase from Clostridium acetobutylicum
ComponentsShort-chain-enoyl-CoA hydratase
KeywordsLYASE / short-chain enoyl-CoA hydratase
Function / homology
Function and homology information


short-chain-enoyl-CoA hydratase / butyrate metabolic process / lyase activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Short-chain-enoyl-CoA hydratase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, E.-J. / Kim, Y.-J. / Kim, K.-J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2014
Title: Structural insights into substrate specificity of crotonase from the n-butanol producing bacterium Clostridium acetobutylicum.
Authors: Kim, E.J. / Kim, Y.J. / Kim, K.J.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short-chain-enoyl-CoA hydratase
B: Short-chain-enoyl-CoA hydratase
C: Short-chain-enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)87,1513
Polymers87,1513
Non-polymers00
Water2,504139
1
A: Short-chain-enoyl-CoA hydratase
B: Short-chain-enoyl-CoA hydratase
C: Short-chain-enoyl-CoA hydratase

A: Short-chain-enoyl-CoA hydratase
B: Short-chain-enoyl-CoA hydratase
C: Short-chain-enoyl-CoA hydratase


  • defined by author&software
  • Evidence: gel filtration, Hexameric structure of CaCRT could be easily generated by applying P3212 crystallographic symmetric operation and size exclusion chromatography confirmed the hexameric nature of CaCRT.
  • 174 kDa, 6 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)174,3036
Polymers174,3036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x+y-1,y,-z-1/31
Buried area30950 Å2
ΔGint-191 kcal/mol
Surface area50450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.673, 78.673, 210.703
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11C-303-

HOH

-
Components

#1: Protein Short-chain-enoyl-CoA hydratase / 3-hydroxybutyryl-CoA dehydratase / Crotonase


Mass: 29050.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: crt, CA_C2712 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P52046, short-chain-enoyl-CoA hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M Sodium cacodylate pH 6.5, 0.2M Lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97956 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2010
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37287 / % possible obs: 97.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Χ2: 0.939 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.242.80.26916840.598189.3
2.24-2.283.20.26317360.552192.2
2.28-2.323.30.27518150.551194.9
2.32-2.373.50.24818550.569196.5
2.37-2.423.90.23318080.52196.7
2.42-2.483.80.21918420.616196.2
2.48-2.543.90.21118500.559196.9
2.54-2.6140.18118540.673197.5
2.61-2.694.20.1718200.747197
2.69-2.774.30.14918750.64197.7
2.77-2.874.40.1318531.014197.7
2.87-2.994.50.1118960.661198.2
2.99-3.124.80.09718801.148198.4
3.12-3.295.10.08118960.891198.4
3.29-3.495.40.06518850.969199.3
3.49-3.765.40.05519431.366199.4
3.76-4.145.70.04419151.209199.3
4.14-4.745.70.0419141.248199.2
4.74-5.975.70.04119541.042199
5.97-505.60.03520121.634198.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJ3

1mj3


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.246 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.237
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1866 5 %RANDOM
Rwork0.1888 ---
obs0.1921 35417 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.27 Å2 / Biso mean: 35.211 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å2-0 Å2
2--0.86 Å20 Å2
3----2.78 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5727 0 0 139 5866
Biso mean---32.96 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195778
X-RAY DIFFRACTIONr_bond_other_d0.0010.025814
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.987758
X-RAY DIFFRACTIONr_angle_other_deg0.852313389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.22525.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1631533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021188
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 120 -
Rwork0.267 2377 -
all-2497 -
obs--89.34 %

+
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