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Yorodumi- PDB-1hlp: STRUCTURAL FEATURES STABILIZING HALOPHILIC MALATE DEHYDROGENASE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hlp | ||||||
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Title | STRUCTURAL FEATURES STABILIZING HALOPHILIC MALATE DEHYDROGENASE FROM AN ARCHAEBACTERIUM | ||||||
Components | MALATE DEHYDROGENASE | ||||||
Keywords | DEHYDROGENASE / HALOPHILIC | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | ||||||
Authors | Dym, O. / Mevarech, M. / Sussman, J.L. | ||||||
Citation | Journal: Science / Year: 1995 Title: Structural Features That Stabilize Halophilic Malate Dehydrogenase from an Archaebacterium. Authors: Dym, O. / Mevarech, M. / Sussman, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hlp.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hlp.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 1hlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hlp_validation.pdf.gz | 937.4 KB | Display | wwPDB validaton report |
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Full document | 1hlp_full_validation.pdf.gz | 982.8 KB | Display | |
Data in XML | 1hlp_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 1hlp_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hlp ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hlp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.904838, 0.001957, 0.425752), Vector: Details | THE PROTEIN FORMS A TETRAMER. THE FOLLOWING TRANSFORMATION CAN BE USED TO GENERATE THE TETRAMER FROM THE COORDINATES GIVEN: SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 61.72839 | |
-Components
#1: Protein | Mass: 32706.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloarcula marismortui (Halophile) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: Q07841, malate dehydrogenase #2: Chemical | Sequence details | THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE SEQUENCE OF J. CHROBOCZEK ET AL., ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE SEQUENCE OF J. CHROBOCZEK | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 69.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 12508 / % possible obs: 88.3 % |
Reflection | *PLUS Highest resolution: 3.24 Å / Num. all: 14158 / Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Resolution: 3.2→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 10915 / Rfactor all: 0.182 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.01 |