[English] 日本語
Yorodumi
- PDB-4tvm: Structure of Citrate Synthase from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tvm
TitleStructure of Citrate Synthase from Mycobacterium tuberculosis
ComponentsCitrate synthase
KeywordsTRANSFERASE / Krebs cycle
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / plasma membrane / cytosol
Similarity search - Function
Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain ...Rubrerythrin, domain 2 - #60 / Citrate synthase, type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Rubrerythrin, domain 2 / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
OXALOACETATE ION / : / Citrate synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFerraris, D.M. / Rizzi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union FP7 ProgramSysteMTb HEALTH-F4-2010-241587 Italy
CitationJournal: Proteins / Year: 2015
Title: Structures of citrate synthase and malate dehydrogenase of Mycobacterium tuberculosis.
Authors: Ferraris, D.M. / Spallek, R. / Oehlmann, W. / Singh, M. / Rizzi, M.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Dec 20, 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: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1322
Polymers48,0011
Non-polymers1311
Water64936
1
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2654
Polymers96,0022
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11520 Å2
ΔGint-58 kcal/mol
Surface area31770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.767, 148.767, 182.797
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Citrate synthase


Mass: 48001.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: RVBD_0896 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6XWI3, UniProt: P9WPD5*PLUS, citrate (Si)-synthase
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Citrate synthase crystals grew at 20 degrees Celsius in 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH=8.5, 3.4M 1,6-Hexandiol in a 75/25 protein/reservoir-ratio drop of 1 microlitre and ...Details: Citrate synthase crystals grew at 20 degrees Celsius in 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH=8.5, 3.4M 1,6-Hexandiol in a 75/25 protein/reservoir-ratio drop of 1 microlitre and with a protein concentration of 5.2 mg/ml.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.545
11-2/3H-1/3K+2/3L, -1/3H-2/3K-2/3L, 2/3H-2/3K+1/20.179
11-1/3H+1/3K-2/3L, -K, -4/3H-2/3K+1/3L30.115
111/3H-1/3K+2/3L, -H, -2/3H-4/3K-1/3L40.161
ReflectionResolution: 2.6→47.14 Å / Num. obs: 24114 / % possible obs: 99.92 % / Redundancy: 6.2 % / Net I/σ(I): 7.91

-
Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E6Y

4e6y


Resolution: 2.6→47.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.225 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19405 1290 5.4 %RANDOM
Rwork0.17378 ---
obs0.17494 22819 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.367 Å2
Baniso -1Baniso -2Baniso -3
1-14.13 Å20 Å20 Å2
2--14.13 Å20 Å2
3----28.26 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 9 36 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193041
X-RAY DIFFRACTIONr_bond_other_d0.0020.022856
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9674128
X-RAY DIFFRACTIONr_angle_other_deg0.90236555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6615376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09423.521142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17715483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8271522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213462
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02708
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7645.3871516
X-RAY DIFFRACTIONr_mcbond_other3.7545.3861515
X-RAY DIFFRACTIONr_mcangle_it5.5188.0711888
X-RAY DIFFRACTIONr_mcangle_other5.5168.0721889
X-RAY DIFFRACTIONr_scbond_it3.5935.5631525
X-RAY DIFFRACTIONr_scbond_other3.5945.5631523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4358.2312240
X-RAY DIFFRACTIONr_long_range_B_refined9.550.07612584
X-RAY DIFFRACTIONr_long_range_B_other9.50250.07512571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.593→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 83 -
Rwork0.19 1502 -
obs--88.06 %

+
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