[English] 日本語
Yorodumi
- PDB-9yri: cis-CaaD E114Q mutant with covalent intermediates of the hydratio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yri
Titlecis-CaaD E114Q mutant with covalent intermediates of the hydration and decarboxylation of acetylenecarboxylic acid
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD / acetylenecaarboxylic acid
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: cis-CaaD E114Q mutant
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionNov 5, 2025ID: 9O2P
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase
B: Cis-3-chloroacrylic acid dehalogenase
C: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0666
Polymers55,7783
Non-polymers2883
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-101 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.608, 101.228, 148.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18592.635 Da / Num. of mol.: 3 / Mutation: E114Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VPE5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: (0.05 citric acid, 0.05 BIS-TRIS propane) pH 5 20% w/v PEG 3,352

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.13 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21779 / % possible obs: 92.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.26 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 19.14
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 964 / Rpim(I) all: 0.325

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.8 Å / SU ML: 0.2671 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 3088 9.16 %
Rwork0.2153 30611 -
obs0.2177 21186 75.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 21 105 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01293525
X-RAY DIFFRACTIONf_angle_d1.11454770
X-RAY DIFFRACTIONf_chiral_restr0.0719495
X-RAY DIFFRACTIONf_plane_restr0.0099639
X-RAY DIFFRACTIONf_dihedral_angle_d18.35831263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.3456740.3366701X-RAY DIFFRACTION38.58
2.25-2.260.641830.550655X-RAY DIFFRACTION10.74
2.27-2.310.3416760.2936726X-RAY DIFFRACTION42.41
2.31-2.350.28761060.24861018X-RAY DIFFRACTION54.7
2.35-2.40.31391110.24621033X-RAY DIFFRACTION57.26
2.4-2.440.27821140.24291173X-RAY DIFFRACTION63.49
2.44-2.50.28521280.251309X-RAY DIFFRACTION70.72
2.5-2.560.29581570.23281447X-RAY DIFFRACTION77.26
2.56-2.620.24971550.22951503X-RAY DIFFRACTION82.65
2.62-2.690.29451720.24341622X-RAY DIFFRACTION87.38
2.69-2.770.2841560.24111669X-RAY DIFFRACTION90.35
2.77-2.860.36721810.2661681X-RAY DIFFRACTION90.83
2.86-2.960.23991790.23881730X-RAY DIFFRACTION92.09
2.96-3.080.29061720.24561717X-RAY DIFFRACTION94.97
3.08-3.220.27151590.24981739X-RAY DIFFRACTION93.13
3.22-3.390.26931740.24811715X-RAY DIFFRACTION92.06
3.39-3.60.28021830.22761605X-RAY DIFFRACTION88.47
3.6-3.880.19381210.21421173X-RAY DIFFRACTION63.49
3.88-4.270.18261400.17091492X-RAY DIFFRACTION79.84
4.27-4.880.18071760.16271836X-RAY DIFFRACTION98.72
4.88-6.150.22361770.18271836X-RAY DIFFRACTION98.97
6.15-35.80.16881740.1791831X-RAY DIFFRACTION98.28

+
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