[English] 日本語
Yorodumi
- PDB-7ms3: Crystal structure of R73A mutant of Cg10062 with a covalent inter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ms3
TitleCrystal structure of R73A mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid
Components4-oxalocrotonate tautomerase
KeywordsHYDROLASE / tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNayebi, G.H. / Geiger, J.H. / Draths, K.
CitationJournal: Biochemistry / Year: 2021
Title: Cg10062 Catalysis Forges a Link between Acetylenecarboxylic Acid and Bacterial Metabolism.
Authors: Mathes Hewage, A. / Nayebi Gavgani, H. / Chi, D. / Qiu, B. / Geiger, J.H. / Draths, K.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0422
Polymers18,9521
Non-polymers901
Water00
1
A: 4-oxalocrotonate tautomerase
hetero molecules

A: 4-oxalocrotonate tautomerase
hetero molecules

A: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1276
Polymers56,8563
Non-polymers2703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9130 Å2
ΔGint-44 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.551, 146.551, 146.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

-
Components

#1: Protein 4-oxalocrotonate tautomerase / Cis-3-chloroacrylic acid dehalogenase


Mass: 18952.133 Da / Num. of mol.: 1 / Mutation: R73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Gene: APT58_00490, AUO95_07180, CS176_0056, FM102_14895, KaCgl_17770, KbCgl_30240
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S2T163
#2: Chemical ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.92 Å3/Da / Density % sol: 82.23 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM ammonium fluoride, 10% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→35.54 Å / Num. obs: 11178 / % possible obs: 98.69 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.055 / Rrim(I) all: 0.18 / Net I/σ(I): 10.4
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 1086 / CC1/2: 0.45 / Rpim(I) all: 0.65 / % possible all: 99.91

-
Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MS0

7ms0


Resolution: 3→35.54 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 --
Rwork0.2035 --
obs-11174 98.669 %
Refinement stepCycle: LAST / Resolution: 3→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 6 0 1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221207
X-RAY DIFFRACTIONf_angle_d1.21121640
X-RAY DIFFRACTIONf_chiral_restr0.0646182
X-RAY DIFFRACTIONf_plane_restr0.0071212
X-RAY DIFFRACTIONf_dihedral_angle_d30.0671449

+
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