+Open data
-Basic information
Entry | Database: PDB / ID: 3enj | ||||||
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Title | Structure of Pig Heart Citrate Synthase at 1.78 A resolution | ||||||
Components | Citrate synthase | ||||||
Keywords | LYASE / TRANSFERASE / disulfide exchange / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for High-Throughput Structural Biology / CHTSB / Methylation / Mitochondrion / Transit peptide / Tricarboxylic acid cycle | ||||||
Function / homology | Function and homology information citrate (Si)-synthase / citrate synthase activity / Citric acid cycle (TCA cycle) / citrate (Si)-synthase activity / citrate metabolic process / Mitochondrial protein degradation / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT PLACEMENT IN SAME UNIT CELL / Resolution: 1.78 Å | ||||||
Authors | Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A. / Center for High-Throughput Structural Biology (CHTSB) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of pig heart citrate synthase at 1.78 A resolution. Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A. #1: Journal: CRYST.GROWTH DES. / Year: 2008 Title: Progress in the Development of an Alternative Approach to Macromolecular Crystallization Authors: Larson, S.B. / Day, J.S. / Nguyen, C. / Cudney, R. / McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3enj.cif.gz | 357.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3enj.ent.gz | 298.4 KB | Display | PDB format |
PDBx/mmJSON format | 3enj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3enj_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 3enj_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 3enj_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3enj_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/3enj ftp://data.pdbj.org/pub/pdb/validation_reports/en/3enj | HTTPS FTP |
-Related structure data
Related structure data | 1ctsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY THE TWO FOLD AXIS: 1-Y, -X, 1/2-Z |
-Components
#1: Protein | Mass: 48977.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00889, citrate (Si)-synthase |
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#2: Chemical | ChemComp-CYS / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.27 % |
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Crystal grow | Temperature: 295 K / pH: 8.2 Details: 25% PEG 3350 in H2O in the presence of cystamine HCl, aspartame, benzamidine HCl and Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97839 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97839 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→41.56 Å / Num. obs: 56320 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 6.35 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT PLACEMENT IN SAME UNIT CELL Starting model: PDB ENTRY 1CTS Resolution: 1.78→41.56 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 8.413 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH ...Details: HYDROGENS FOR ALL NON-WATER MOLECULES HAVE BEEN ADDED IN THE RIDING POSITION AND ADJUSTED TO AVOID STERIC PROBLEMS. OCCUPANCIES FOR HYDROGENS WERE SET TO THE OCCUPANCY OF THE ATOM TO WHICH THE HYDROGEN WAS ATTACHED. THE CYSTEAMINE (CYS A 500) COVALENTLY ATTACHED BY A DISULFIDE BOND TO CYSTEINE 184 WAS MODELED AS A CYSTEINE WITH ATOMS C AND O MISSING (SEE REMARK 610). COMMENT ON REMARK 500 BAD TORSION ANGLES. SIDE CHAIN DENSITY IS WEAK AND SIDE CHAIN MAY BE DISORDERED FOR ASP A 295. DENSITY FOR THE LOOP CONTAINING LYS A 366 IS NOT HIGHLY RESOLVED. ARG A 421 IS DISORDERED. ALL OTHERS IN THIS LIST ARE IN WELL-DEFINED DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.83 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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