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- PDB-4xgh: X-ray Crystal Structure of Citrate Synthase from Burkholderia tha... -

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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


citrate (Si)-synthase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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: 0

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

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Phasing

PhasingMethod: molecular replacement

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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

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