[English] 日本語
Yorodumi
- PDB-6ijk: Enoyl-CoA hydratase/isomerase family protein from Cupriavidus nec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ijk
TitleEnoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / isomerase
Function / homologyenoyl-CoA hydratase / Enoyl-CoA hydratase, C-terminal / enoyl-CoA hydratase activity / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Enoyl-CoA hydratase
Function and homology information
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016M3D3A1A01913269 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M1A2A2087631 Korea, Republic Of
National Research Foundation (Korea)NRF-2018H1A2A1061751 Korea, Republic Of
CitationJournal: Biotechnol. Bioprocess Eng. / Year: 2019
Title: Crystal structure of a novel type isomerase of enoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16
Authors: Seo, H. / Kim, K.-J.
History
DepositionOct 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_id_ISSN
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: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)64,7192
Polymers64,7192
Non-polymers00
Water84747
1
A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)97,0783
Polymers97,0783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10710 Å2
ΔGint-80 kcal/mol
Surface area29110 Å2
MethodPISA
2
B: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)97,0783
Polymers97,0783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10820 Å2
ΔGint-80 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.941, 132.941, 44.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein Enoyl-CoA hydratase


Mass: 32359.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria)
Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_B0756 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0K371, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 550 MME, NaCl, Bicine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 22, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57392 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rsym value: 0.09 / Net I/σ(I): 41.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 8.5 / CC1/2: 0.874

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZAI

5zai


Resolution: 2→35.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.663 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 2887 5 %RANDOM
Rwork0.2025 ---
obs0.204 55042 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.29 Å2 / Biso mean: 33.317 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å2-0 Å2
2---0.49 Å2-0 Å2
3---1.58 Å2
Refinement stepCycle: final / Resolution: 2→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 0 47 4127
Biso mean---34.96 -
Num. residues----538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173897
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6335663
X-RAY DIFFRACTIONr_angle_other_deg1.4181.5718949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8325536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.14519.737228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01515639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5121544
X-RAY DIFFRACTIONr_chiral_restr0.0860.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 223 -
Rwork0.262 3940 -
all-4163 -
obs--97.15 %

+
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://pdbjlvh1.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