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- PDB-6s87: Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 6s87
TitleCrystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.
ComponentsCitrate synthase
KeywordsTRANSFERASE / 2-methlycitrate synthase / PrpC / propionate metabolism / methylcitrate cycle
Function / homology
Function and homology information


2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / citrate synthase activity / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytoplasm
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase
Similarity search - Domain/homology
OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M019411/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R005435/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.
Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M.
History
DepositionJul 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,65011
Polymers166,9664
Non-polymers6847
Water6,323351
1
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7595
Polymers83,4832
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-39 kcal/mol
Surface area26970 Å2
MethodPISA
2
C: Citrate synthase
D: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8906
Polymers83,4832
Non-polymers4074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-38 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.640, 86.760, 161.840
Angle α, β, γ (deg.)90.000, 95.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Citrate synthase


Mass: 41741.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: prpC, PA0795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 100 mM Bis-Tris pH 5.5, 15-25% PEG3350, 40 mM D-Xylose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.65→27.23 Å / Num. obs: 170245 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 31.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.035 / Rrim(I) all: 0.073 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.694.31.3621.1125370.5780.7471.55799.9
7.38-27.224.20.02191610.0110.02396.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S6F

6s6f


Resolution: 1.65→27.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.86 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.095
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 4622 2.7 %RANDOM
Rwork0.1973 ---
obs0.1978 165599 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.5 Å2 / Biso mean: 29.591 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0 Å20.66 Å2
2--1.94 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.65→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11279 0 45 352 11676
Biso mean--37.78 32.56 -
Num. residues----1431
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 362 -
Rwork0.355 12166 -
all-12528 -
obs--99.82 %

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