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Yorodumi- PDB-2ldb: STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ldb | |||||||||
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Title | STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE | |||||||||
Components | L-LACTATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE(CHOH(D)-NAD(A)) | |||||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / NAD binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | |||||||||
Authors | Piontek, K. / Rossmann, M.G. | |||||||||
Citation | Journal: Proteins / Year: 1990 Title: Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase. Authors: Piontek, K. / Chakrabarti, P. / Schar, H.P. / Rossmann, M.G. / Zuber, H. #1: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1987 Title: Nucleotide Sequences of Lactate Dehydrogenase Genes from the Thermophilic Bacteria Bacillus Stearothermophilus, B. Caldolyticus and B. Caldotenax Authors: Zuelli, F. / Weber, H. / Zuber, H. #2: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallization of Lactate Dehydrogenase from Bacillus Stearothermophilus Authors: Schaer, H.-P. / Zuber, H. / Rossmann, M.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ldb.cif.gz | 249.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ldb.ent.gz | 196.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ldb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ldb_validation.pdf.gz | 818.7 KB | Display | wwPDB validaton report |
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Full document | 2ldb_full_validation.pdf.gz | 973.4 KB | Display | |
Data in XML | 2ldb_validation.xml.gz | 50.3 KB | Display | |
Data in CIF | 2ldb_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/2ldb ftp://data.pdbj.org/pub/pdb/validation_reports/ld/2ldb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 139 IS A CIS PROLINE. | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS CORRESPONDING TO THE THREE ORTHOGONAL MOLECULAR TWO-FOLD SYMMETRY AXES ARE PRESENTED ON THE *MTRIX* RECORDS BELOW. |
-Components
#1: Protein | Mass: 34902.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) References: UniProt: P00344, L-lactate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #4: Sugar | #5: Water | ChemComp-HOH / | Sequence details | THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIALLY FROM 15 - 331. SEE C. ABAD-ZAPATERO, J. P. ...THE RESIDUES IN THIS ENTRY ARE NUMBERED SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.71 % | |||||||||||||||||||||||||
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Crystal grow | Details: THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NAD AND THE ACTIVATOR FBP. THE NAD MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P- ...Details: THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NAD AND THE ACTIVATOR FBP. THE NAD MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P-AXIS. THE P-AXIS INTERSECTS THE ACTIVATOR MOLECULE GIVING RISE TO A STATISTICAL DISORDER (OCCUPANCY 0.5) AS FBP HAS ONLY PSEUDO-TWO-FOLD SYMMETRY. ONE SULFATE (SO4 3) BINDS AT THE SUBSTRATE BINDING SITE. ANOTHER SULFATE (SO4 4) IS CLOSE TO THE R-AXIS INTERFACE. | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusionDetails: taken from Schar, H-P. et al (1982). J. Mol. Biol., 154, 349-353. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. obs: 24793 / % possible obs: 79.8 % / Observed criterion σ(I): 2 / Num. measured all: 76407 / Rmerge(I) obs: 0.109 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→6 Å / Rfactor obs: 0.26 Details: THE ASSIGNMENT OF DONOR AND ACCEPTOR WAS ARBITRARY FOR THE FOLLOWING HYDROGEN BONDS NO7 NAD 1 O3 SO4 3 O3 SO4 3 OD1 ASP 46 O4 SO4 4 O LYS 74 O3 SO4 4 O ALA 45 O3 SO4 4 O GLY 43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 21007 / Rfactor obs: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |