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- PDB-6zu0: Crystal structure of citrate synthase (GltA) from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 6zu0
TitleCrystal structure of citrate synthase (GltA) from Pseudomonas aeruginosa
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate synthase / GltA / TCA cycle
Function / homology
Function and homology information


citrate synthase activity / citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Citrate synthase, type I / Citrate synthase, bacterial-type / 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
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.397 Å
AuthorsWijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M019411/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R005435/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of citrate synthase (GltA) from Pseudomonas aeruginosa
Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
History
DepositionJul 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)286,5356
Polymers286,5356
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40020 Å2
ΔGint-250 kcal/mol
Surface area92880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.746, 80.177, 196.659
Angle α, β, γ (deg.)90.000, 121.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Citrate synthase


Mass: 47755.777 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gltA, PA1580 / Production host: Escherichia coli (E. coli)
References: UniProt: P14165, citrate synthase (unknown stereospecificity)

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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: 5.6 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 2% PEG400, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.39→83.489 Å / Num. obs: 39887 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 80 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.102 / Rrim(I) all: 0.219 / Net I/av σ(I): 4.7 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.4-3.494.51.0211.329410.5660.5361.15799.9
15.21-83.463.80.07312.94900.9860.0430.08699.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E6Y

4e6y


Resolution: 3.397→83.489 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 1894 4.78 %
Rwork0.2377 37695 -
obs0.239 39589 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.02 Å2 / Biso mean: 70 Å2 / Biso min: 46.39 Å2
Refinement stepCycle: final / Resolution: 3.397→83.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19923 0 0 0 19923
Num. residues----2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720418
X-RAY DIFFRACTIONf_angle_d1.30727632
X-RAY DIFFRACTIONf_chiral_restr0.0683011
X-RAY DIFFRACTIONf_plane_restr0.0043593
X-RAY DIFFRACTIONf_dihedral_angle_d14.3557566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3972-3.48220.45881400.3688260397
3.4822-3.57630.37251380.353263899
3.5763-3.68160.53591420.4673263898
3.6816-3.80040.37981350.3473265398
3.8004-3.93620.32821280.26822681100
3.9362-4.09380.3011070.2625271999
4.0938-4.28010.28511360.2292710100
4.2801-4.50580.22271140.22142697100
4.5058-4.78810.24521300.20222716100
4.7881-5.15770.22381190.19592700100
5.1577-5.67660.2311610.2069268199
5.6766-6.49780.21761110.2146275699
6.4978-8.18540.1991760.19052712100
8-100.19151570.1732279199

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