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Yorodumi- PDB-1i0z: HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i0z | ||||||
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Title | HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE | ||||||
Components | L-LACTATE DEHYDROGENASE H CHAIN | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / NAD metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / NAD metabolic process / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Read, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase. Authors: Read, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i0z.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i0z.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/1i0z ftp://data.pdbj.org/pub/pdb/validation_reports/i0/1i0z | HTTPS FTP |
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-Related structure data
Related structure data | 1i10C 5ldhS C: citing same article (ref.) 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 biological assembly is a tetramer generated from the dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 36548.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Organ: HEART / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07195, L-lactate dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.74 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: protein solution: 15 mg/ml H4-ldh, 50 mM Na-Hepes pH 7.5, 2.5 mM NADH, 1 mM oxamate. Well solution: 21% PEG 8k, 100 mM Na-HEPES ph 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 7, 1999 |
Radiation | Monochromator: platinum mirrors/Ge 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 39237 / Num. obs: 37680 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.31 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.25 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 8.5 / Num. unique all: 4400 / % possible all: 91.1 |
Reflection shell | *PLUS % possible obs: 91.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ldh Resolution: 2.1→20 Å / SU B: 4.848 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.247 / ESU R Free: 0.197 / Stereochemistry target values: Engh & Huber Details: METHOD USED FOR BULK SOLVENT MODELLING: BABINET MODEL WITH MASK. PARAMETERS FOR MASK CALCULATION: VDW PROBE RADIUS = 1.40, ION PROBE RADIUS = 0.80, SHRINKAGE RADIUS = 0.80.
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Displacement parameters | Biso mean: 19.533 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20 /
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.179 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.177 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |