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Yorodumi- PDB-1hpc: REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hpc | ||||||
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Title | REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FORMS OF THE H-PROTEIN, A LIPOAMIDE-CONTAINING PROTEIN OF THE GLYCINE DECARBOXYLASE | ||||||
Components | H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM | ||||||
Keywords | TRANSIT PEPTIDE | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system / mitochondrion Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Pares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Refined structures at 2 and 2.2 A resolution of two forms of the H-protein, a lipoamide-containing protein of the glycine decarboxylase complex. Authors: Pares, S. / Cohen-Addad, C. / Sieker, L.C. / Neuburger, M. / Douce, R. #1: Journal: Nat.Struct.Biol. / Year: 1995 Title: The Lipoamide Arm in the Glycine Decarboxylase Complex is not Freely Swinging Authors: Cohen-Addad, C. / Pares, S. / Sieker, L. / Neuburger, M. / Douce, R. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: X-Ray Structure Determination at 2.6 Angstroms Resolution of a Lipoate-Containing Protein: The H-Protein of the Glycine Decarboxylase Complex from Pea Leaves Authors: Pares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallographic Data for H-Protein from the Glycine Decarboxylase Complex Authors: Sieker, L. / Cohen-Addad, C. / Neuburger, M. / Douce, R. #4: Journal: Biochem.J. / Year: 1990 Title: Cdna Cloning, Primary Structure and Gene Expression for H-Protein, a Component of the Glycine-Cleavage System (Glycine Decarboxylase) of Pea (Pisum Sativum) Leaf Mitochondria Authors: Macherel, D. / Lebrun, M. / Gagnon, J. / Neuburger, M. / Douce, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hpc.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hpc.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hpc ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hpc | HTTPS FTP |
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-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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.3895, 0.566, 0.726), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 13962.464 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) References: UniProt: P16048, glycine dehydrogenase (aminomethyl-transferring) #2: Chemical | ChemComp-LPB / | #3: Chemical | ChemComp-LPA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.99 % | |||||||||||||||
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Crystal | *PLUS Density % sol: 45 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 281 K / pH: 5.2 / Method: vapor diffusion | |||||||||||||||
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: 17031 / % possible obs: 92 % |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 87067 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 80 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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