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Yorodumi- PDB-1amz: CHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1amz | ||||||
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Title | CHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE | ||||||
Components | CITRATE SYNTHASE | ||||||
Keywords | OXO-ACID-LYASE / TRICARBOXYLIC ACID CYCLE / ALLOSTERIC ENZYME | ||||||
Function / homology | Function and homology information citrate (Si)-synthase / The tricarboxylic acid cycle / citrate synthase activity / citrate (Si)-synthase activity / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.8 Å | ||||||
Authors | Usher, K.C. / Remington, S.J. | ||||||
Citation | Journal: To be Published Title: Mechanisms of Enzyme-Catalyzed Deprotonation of Acetyl-Coenzyme A Authors: Schwartz, B. / Vogel, K.W. / Usher, K.C. / Narasimhan, C. / Miziorko, H.M. / Remington, S.J. / Drueckhammer, D.G. #1: Journal: Biochemistry / Year: 1994 Title: A Very Short Hydrogen Bond Provides Only Moderate Stabilization of an Enzyme-Inhibitor Complex of Citrate Synthase Authors: Usher, K.C. / Remington, S.J. / Martin, D.P. / Drueckhammer, D.G. #2: Journal: Biochemistry / Year: 1990 Title: Proposed Mechanism for the Condensation Reaction of Citrate Synthase: 1.9-A Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A Authors: Karpusas, M. / Branchaud, B. / Remington, S.J. #3: Journal: J.Mol.Biol. / Year: 1984 Title: Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzyme A Authors: Wiegand, G. / Remington, S. / Deisenhofer, J. / Huber, R. #4: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 A Resolution Authors: Remington, S. / Wiegand, G. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1amz.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1amz.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1amz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1amz ftp://data.pdbj.org/pub/pdb/validation_reports/am/1amz | HTTPS FTP |
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-Related structure data
Related structure data | 1al6C 1cshS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 48174.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: INNER MATRIX / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P23007, EC: 4.1.3.7 |
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#2: Chemical | ChemComp-MLT / |
#3: Chemical | ChemComp-NMX / |
#4: 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: 2.4 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 6 Details: CRYSTALLIZED FROM 1.01M NA MALATE, PH 6.0 2 MM NITROMETHYLDETHIA COENZYME A THE CELL ANGLE BETA IS DEFINED AS THE ACUTE ANGLE FOR CONSISTENCY WITH PREVIOUS PDB ENTRIES OF CITRATE SYNTHASE IN THIS SPACE GROUP |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 12, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 36528 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.8→1.94 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.1 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR SUBSTITUTION Starting model: PDB ENTRY 1CSH Resolution: 1.8→25 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 680 Å2 / ksol: 1.07 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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