[English] 日本語
Yorodumi
- PDB-4xgh: X-ray Crystal Structure of Citrate Synthase from Burkholderia tha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xgh
TitleX-ray Crystal Structure of Citrate Synthase from Burkholderia thailandensis
ComponentsCitrate synthase
KeywordsTRANSFERASE / SSGCID / citrate synthase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


: / tricarboxylic acid cycle / cytoplasm
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
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: X-ray Crystal Structure of Citrate Synthase from Burkholderia thailandensis
Authors: Fairman, J.W. / Lukacs, C.M. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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)51,58310
Polymers50,8201
Non-polymers7639
Water3,639202
1
A: Citrate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)309,49660
Polymers304,9216
Non-polymers4,57554
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area50720 Å2
ΔGint-646 kcal/mol
Surface area85740 Å2
MethodPISA
2
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,74830
Polymers152,4603
Non-polymers2,28827
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7760 Å2
ΔGint-240 kcal/mol
Surface area60470 Å2
MethodPISA
3
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,16520
Polymers101,6402
Non-polymers1,52518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area14120 Å2
ΔGint-183 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.250, 120.250, 219.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-504-

SO4

21A-504-

SO4

31A-619-

HOH

41A-621-

HOH

51A-632-

HOH

61A-634-

HOH

71A-666-

HOH

Detailsbiological unit is a monomer

-
Components

#1: Protein Citrate synthase


Mass: 50820.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Gene: gltA, BTH_II0665 / Plasmid: ButhA.00896.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T7I5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG screen H2: 1.0 M ammonium sulfate, 1% PEG3350, 0.1 M BIS-TRIS pH 5.50
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 35644 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 34.65 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.056 / Χ2: 0.982 / Net I/σ(I): 18.65 / Num. measured all: 110577
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.150.8360.562.448152262026180.68199.9
2.15-2.210.8760.452.917978256425550.54699.6
2.21-2.280.8970.3563.697711248324690.43399.4
2.28-2.350.9460.2714.637597243624280.32999.7
2.35-2.420.9550.2325.477223231923130.28299.7
2.42-2.510.9690.186.567135228722820.21899.8
2.51-2.60.9750.1468.196874220521990.17799.7
2.6-2.710.9850.11310.126619212121150.13799.7
2.71-2.830.9910.08812.416278202120160.10799.8
2.83-2.970.9930.0715.796059195319460.08599.6
2.97-3.130.9970.0520.425786185918550.06199.8
3.13-3.320.9980.03725.815421174917440.04599.7
3.32-3.550.9990.0332.025070166016470.03699.2
3.55-3.830.9990.02538.194704154515310.0399.1
3.83-4.20.9990.02145.714316144314230.02598.6
4.2-4.70.9990.01951.133801127812640.02398.9
4.7-5.420.9990.01852.373385116311340.02297.5
5.42-6.640.9990.01752.5829259839530.0296.9
6.64-9.3910.01361.3523177787470.01696
9.3910.0117112264574050.01388.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L96

3l96
PDB Unreleased entry


Resolution: 2.1→48.573 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 1744 4.9 %RANDOM
Rwork0.2081 33862 --
obs0.2092 35606 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.96 Å2 / Biso mean: 51.8795 Å2 / Biso min: 19.46 Å2
Refinement stepCycle: final / Resolution: 2.1→48.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 42 202 3128
Biso mean--92.43 47.98 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022984
X-RAY DIFFRACTIONf_angle_d0.5844059
X-RAY DIFFRACTIONf_chiral_restr0.021453
X-RAY DIFFRACTIONf_plane_restr0.003530
X-RAY DIFFRACTIONf_dihedral_angle_d10.1611040
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.16180.33511490.28232775292499
2.1618-2.23160.30721460.26982783292999
2.2316-2.31140.29811520.2482796294899
2.3114-2.40390.26131400.228628272967100
2.4039-2.51330.26811300.223228192949100
2.5133-2.64580.22521370.215228302967100
2.6458-2.81160.27591400.221728352975100
2.8116-3.02860.24051570.214128052962100
3.0286-3.33330.23471430.21228462989100
3.3333-3.81550.20261540.18942821297599
3.8155-4.80650.20061430.17312878302199
4.8065-48.58640.20681530.20892847300096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.48220.1751-0.76130.734-0.26761.9811-0.130.1311-0.241-0.00360.02380.10990.2019-0.44370.01660.2417-0.01150.02310.3937-0.0940.261725.814131.46485.3551
22.97890.8491-0.50741.67880.83763.0228-0.0341-0.13230.31080.08120.0030.0875-0.2543-0.07840.05160.26960.04930.02180.30370.00020.270136.312239.743489.9839
31.9525-1.45320.0226.8778-0.3821.77660.2579-0.52031.17190.21240.0960.6234-0.9922-0.3968-0.23510.73670.2130.12490.5873-0.18440.939127.611855.8905100.2092
40.33690.22990.6582-0.00770.11063.2979-0.1146-0.16970.1556-0.1222-0.10950.0979-0.325-0.64110.2620.3230.0814-0.01160.4671-0.10090.384325.942942.189679.6889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 185 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 186 through 282 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 333 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 433 )A0

+
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