[English] 日本語
Yorodumi
- PDB-2qbv: Crystal Structure of Intracellular Chorismate Mutase from Mycobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qbv
TitleCrystal Structure of Intracellular Chorismate Mutase from Mycobacterium Tuberculosis
ComponentsCHORISMATE MUTASE
KeywordsISOMERASE / chorismate mutase / tuberculosis / intracellular / helical / dimeric
Function / homology
Function and homology information


aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Chorismate mutase, high GC Gram-positive bacteria/archaeal / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Chorismate mutase, high GC Gram-positive bacteria/archaeal / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Intracellular chorismate mutase / Intracellular chorismate mutase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLadner, J.E. / Reddy, P.T. / Kim, S.K. / Reddy, S.-K. / Nelson, B.C.
CitationJournal: Febs J. / Year: 2008
Title: A comparative biochemical and structural analysis of the intracellular chorismate mutase (Rv0948c) from Mycobacterium tuberculosis H(37)R(v) and the secreted chorismate mutase (y2828) from Yersinia pestis.
Authors: Kim, S.K. / Reddy, S.K. / Nelson, B.C. / Robinson, H. / Reddy, P.T. / Ladner, J.E.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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: CHORISMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)10,1081
Polymers10,1081
Non-polymers00
Water84747
1
A: CHORISMATE MUTASE

A: CHORISMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)20,2162
Polymers20,2162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3910 Å2
ΔGint-28 kcal/mol
Surface area8640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.860, 59.860, 47.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe molecule is a homodimer. The second chain of the dimer is generated by the symmetry operation y,x,-z and shifted along the c-axis by one c length (47.52).

-
Components

#1: Protein CHORISMATE MUTASE


Mass: 10107.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0948c / Plasmid: pG58 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P64767, UniProt: P9WIC1*PLUS, chorismate mutase
#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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 20% polyethylene glycol 400, 0.1M tris pH 8.6, 0.2M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007 / Details: msc blue confocal
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.33 Å / Num. obs: 6192 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.056 / Χ2: 0.94 / Net I/σ(I): 25.3 / Scaling rejects: 857
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 7 / Num. measured all: 10903 / Num. unique all: 594 / Χ2: 1.11 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YBZ

1ybz


Resolution: 2→19.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.712 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 295 4.8 %RANDOM
Rwork0.219 ---
obs0.222 6191 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2---2.01 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms573 0 0 47 620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022613
X-RAY DIFFRACTIONr_angle_refined_deg1.9852.019823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2220.34529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51515135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1451513
X-RAY DIFFRACTIONr_chiral_restr0.1190.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02447
X-RAY DIFFRACTIONr_nbd_refined0.2180.2252
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.214
X-RAY DIFFRACTIONr_mcbond_it1.3061.5398
X-RAY DIFFRACTIONr_mcangle_it2.0452601
X-RAY DIFFRACTIONr_scbond_it3.1983243
X-RAY DIFFRACTIONr_scangle_it5.2324.5217
LS refinement shellResolution: 2→2.107 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 41 -
Rwork0.241 815 -
obs-856 100 %

+
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