[English] 日本語
Yorodumi
- PDB-9nfh: Native cis-CaaD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nfh
TitleNative cis-CaaD
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / cis-CaaD / Tautomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / ACETATE ION / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Native cis-CaaD
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,6272
Polymers18,5681
Non-polymers591
Water1,47782
1
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8806
Polymers55,7033
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8060 Å2
ΔGint-43 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.964, 59.964, 58.565
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-332-

HOH

31A-375-

HOH

-
Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 18567.582 Da / Num. of mol.: 1
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.18 M ammonium acetate 16% 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: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 27976 / % possible obs: 99.8 % / Redundancy: 9.4 % / Biso Wilson estimate: 16.17 Å2 / Rpim(I) all: 0.029 / Net I/σ(I): 32.48
Reflection shellResolution: 1.32→1.34 Å / Num. unique obs: 1052 / Rpim(I) all: 0.592

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→29.98 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 1994 7.13 %
Rwork0.1905 25957 -
obs0.1921 27951 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.65 Å2
Refinement stepCycle: LAST / Resolution: 1.32→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 4 82 1009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072947
X-RAY DIFFRACTIONf_angle_d1.31911279
X-RAY DIFFRACTIONf_chiral_restr0.146136
X-RAY DIFFRACTIONf_plane_restr0.0147170
X-RAY DIFFRACTIONf_dihedral_angle_d6.2604128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.31741360.29151813X-RAY DIFFRACTION98.09
1.36-1.390.281420.27241863X-RAY DIFFRACTION100
1.39-1.430.32781430.28961831X-RAY DIFFRACTION99.9
1.43-1.480.25751400.21391854X-RAY DIFFRACTION100
1.48-1.530.22911400.18281853X-RAY DIFFRACTION99.95
1.53-1.590.21131440.17781837X-RAY DIFFRACTION100
1.59-1.670.17731430.17051865X-RAY DIFFRACTION99.95
1.67-1.750.22591450.18261854X-RAY DIFFRACTION100
1.75-1.860.18541380.17981859X-RAY DIFFRACTION100
1.86-2.010.18161430.17761855X-RAY DIFFRACTION100
2.01-2.210.22781450.18421854X-RAY DIFFRACTION100
2.21-2.530.20221460.18961870X-RAY DIFFRACTION100
2.53-3.180.20711410.20321856X-RAY DIFFRACTION99.55
3.19-29.980.211480.17931893X-RAY DIFFRACTION99.66

+
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