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- PDB-4e6y: Type II citrate synthase from Vibrio vulnificus. -

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Basic information

Entry
Database: PDB / ID: 4e6y
TitleType II citrate synthase from Vibrio vulnificus.
ComponentsCitrate synthase
KeywordsTRANSFERASE / structural genomics / type II citrate synthase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


citrate (Si)-synthase activity / tricarboxylic acid cycle / membrane => GO:0016020 / 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
FORMIC ACID / Citrate synthase / Citrate synthase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOsipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Type II citrate synthase from Vibrio vulnificus.
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5935
Polymers49,4091
Non-polymers1844
Water90150
1
A: Citrate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)297,55630
Polymers296,4516
Non-polymers1,10524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area45080 Å2
ΔGint-270 kcal/mol
Surface area95900 Å2
2
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,18510
Polymers98,8172
Non-polymers3688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13170 Å2
ΔGint-80 kcal/mol
Surface area33820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.717, 109.717, 153.649
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

Detailsbased on PISA

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Components

#1: Protein Citrate synthase


Mass: 49408.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: gltA, VV1_0162 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DFP4, UniProt: A0A3Q0L1H4*PLUS, citrate (Si)-synthase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium formate, 20 % PEG-3350, 20 mM HEPES buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→45.4 Å / Num. all: 19591 / Num. obs: 19591 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.4 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.146 / Χ2: 2.182 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.5417.40.9394.79581.058100
2.54-2.5917.30.8119461.148100
2.59-2.6417.40.6869521.181100
2.64-2.6917.50.6059711.266100
2.69-2.7517.30.5359481.3100
2.75-2.8217.60.469651.388100
2.82-2.8917.50.4529551.433100
2.89-2.9617.60.3399631.682100
2.96-3.0517.70.3159571.782100
3.05-3.1517.70.2499651.912100
3.15-3.2617.70.2199712.066100
3.26-3.3917.70.1879692.293100
3.39-3.5517.60.1649682.469100
3.55-3.7317.60.1459752.578100
3.73-3.9717.40.139812.589100
3.97-4.2717.40.1169962.72100
4.27-4.717.40.1079962.797100
4.7-5.3817.30.10610033.018100
5.38-6.7816.90.10810344.028100
6.78-5015.80.08311184.62698.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3l96

3l96
PDB Unreleased entry


Resolution: 2.5→45.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.645 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.407 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 996 5.1 %RANDOM
Rwork0.1886 ---
all0.1907 19512 --
obs0.1907 19512 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.08 Å2 / Biso mean: 52.4796 Å2 / Biso min: 25.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å20 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 12 50 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023465
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9544692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8923.476164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4891523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212667
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 60 -
Rwork0.253 1179 -
all-1239 -
obs-1239 99.6 %
Refinement TLS params.Method: refined / Origin x: 20.9121 Å / Origin y: 25.7548 Å / Origin z: 13.5515 Å
111213212223313233
T0.0223 Å2-0.0122 Å20.0002 Å2-0.0449 Å2-0.0019 Å2--0.0412 Å2
L0.4289 °20.1203 °20.1409 °2-0.7141 °2-0.2855 °2--0.9798 °2
S-0.0145 Å °0.0256 Å °0.0013 Å °-0.0245 Å °-0.0259 Å °-0.1559 Å °-0.061 Å °0.2024 Å °0.0404 Å °

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