+Open data
-Basic information
Entry | Database: PDB / ID: 1dxm | ||||||
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Title | Reduced form of the H protein from glycine decarboxylase complex | ||||||
Components | H PROTEIN | ||||||
Keywords | OXIDOREDUCTASES(ACTING ON CH-NH2 DONOR) / GLYCINE DECARBOXYLASE / MITOCHONDRIA | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Faure, M. / Cohen-Addad, C. / Neuburger, M. / Douce, R. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2000 Title: Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins Authors: Faure, M. / Bourguignon, J. / Neuburger, M. / Macherel, D. / Sieker, L. / Ober, R. / Kahn, R. / Cohen-Addad, C. / Douce, R. #1: Journal: Biochimie / Year: 1997 Title: Structural Studies of the Glycine Decarboxylase Complex from Pea Leaf Mitochondria Authors: Cohen-Addad, C. / Faure, M. / Neuburger, M. / Ober, R. / Sieker, L. / Bourguignon, J. / Macherel, D. / Douce, R. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: The Lipoamide Arm in the Glycine Decarboxylase is not Freely Swinging Authors: Cohen-Addad, C. / Pares, S. / Sieker, L. / Neuburger, M. / Douce, R. #3: 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. / 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 | 1dxm.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxm.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxm_validation.pdf.gz | 388 KB | Display | wwPDB validaton report |
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Full document | 1dxm_full_validation.pdf.gz | 389.3 KB | Display | |
Data in XML | 1dxm_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1dxm_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxm ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxm | HTTPS FTP |
-Related structure data
Related structure data | 1dxlC 1hpcS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.39443, 0.54761, 0.73794), Vector: Details | BIOLOGICAL_UNIT: MONOMERTHE GLYCINE CLEAVAGE SYSTEM IS COMPOSED OF FOUR PROTEINS:P, T, L, AND H. THE H CHAIN WAS STUDIED HERE. THIS COMPONENTSHUTTLES THE METHYLAMINE GROUP OF GLYCINE FROM THE P PROTEINTO THE T PROTEIN. THE H CHAIN CONTAINS A COVALENTLY-BOUNDLIPOYL COFACTOR. | |
-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) / Organ: LEAF / Organelle: MITOCHONDRIA / Plasmid: PET-HM / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16048 #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.67 % | ||||||||||||||||||||
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Crystal grow | pH: 5.2 Details: 50 % AMMONIUM SULFATE, 100 MM TRIS MALEATE PH 5.2, 2 MM TCEP (TRIS CARBOXYETHYL PHOSPHINE) | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 7808 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 47.6 Å2 / Rsym value: 0.11 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 98.3 |
Reflection | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HPC Resolution: 2.6→40 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1374190.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.358993 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.207 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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