[English] 日本語
Yorodumi
- PDB-3mf7: Crystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mf7
TitleCrystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / beta-alpha-beta motif / tautomerase / dehalogenase / cis-3-chloroacrylic acid dehalogenase / Isomerase
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGuo, Y. / Serrano, H. / Ernst, S.R. / Johnson Jr., W.H. / Hackert, M.L. / Whitman, C.P.
CitationJournal: Bioorg.Chem. / Year: 2011
Title: Crystal structures of native and inactivated cis-3-chloroacrylic acid dehalogenase: Implications for the catalytic and inactivation mechanisms.
Authors: Guo, Y. / Serrano, H. / Johnson, W.H. / Ernst, S. / Hackert, M.L. / Whitman, C.P.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)16,7331
Polymers16,7331
Non-polymers00
Water2,108117
1
A: Cis-3-chloroacrylic acid dehalogenase

A: Cis-3-chloroacrylic acid dehalogenase

A: Cis-3-chloroacrylic acid dehalogenase


Theoretical massNumber of molelcules
Total (without water)50,1983
Polymers50,1983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
Buried area7110 Å2
ΔGint-42 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.783, 96.783, 96.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

21A-244-

HOH

-
Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 16732.590 Da / Num. of mol.: 1 / Fragment: UNP residues 2-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: Q6VPE5, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.6
Details: three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, ...Details: three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, temperature 298K, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 25, 2005
RadiationMonochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 19123 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.063 / Χ2: 3.096 / Net I/σ(I): 24
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.62-1.684.40.24117512.11791.2
1.68-1.754.60.20319232.289100
1.75-1.824.70.16619122.5899.9
1.82-1.924.40.13318742.97499.5
1.92-2.044.60.10619353.347100
2.04-2.24.70.08619323.39699.9
2.2-2.424.10.07419043.78199.4
2.42-2.774.80.06419373.459100
2.77-3.494.80.05219623.566100
3.49-504.60.04319933.33699.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MF8

3mf8


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.282 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 935 5.2 %RANDOM
Rwork0.186 ---
obs0.188 17952 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.24 Å2 / Biso mean: 9.866 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 0 117 1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021932
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9311259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67923.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53415147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.029157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02720
X-RAY DIFFRACTIONr_nbd_refined0.270.2401
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.222
X-RAY DIFFRACTIONr_mcbond_it0.8641.5596
X-RAY DIFFRACTIONr_mcangle_it1.2822922
X-RAY DIFFRACTIONr_scbond_it2.2813372
X-RAY DIFFRACTIONr_scangle_it3.384.5337
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 65 -
Rwork0.21 1251 -
all-1316 -
obs--100 %

+
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