+Open data
-Basic information
Entry | Database: PDB / ID: 1vzm | ||||||
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Title | OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS | ||||||
Components | OSTEOCALCIN | ||||||
Keywords | CALCIUM-BINDING PROTEIN / OSTEOCALCIN / BONE GLA PROTEIN / BGP / HYDROXYAPATITE / GAMMA CARBOXYL GLUTAMIC ACID / VITAMIN K / BONE / MINERALIZATION | ||||||
Function / homology | Function and homology information response to vitamin K / regulation of bone mineralization / bone mineralization / regulation of cellular response to insulin stimulus / bone development / collagen-containing extracellular matrix / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ARGYROSOMUS REGIUS (meagre) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å | ||||||
Authors | Frazao, C. / Simes, D.C. / Coelho, R. / Alves, D. / Williamson, M.K. / Price, P.A. / Cancela, M.L. / Carrondo, M.A. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Evidence of a Fourth Gla Residue in Fish Osteocalcin: Biological Implications Authors: Frazao, C. / Simes, D.C. / Coelho, R. / Alves, D. / Williamson, M.K. / Price, P.A. / Cancela, M.L. / Carrondo, M.A. #1: Journal: J.Bone Miner.Res. / Year: 2003 Title: Purification of Matrix Gla Protein from a Marine Teleost Fish, Argyrosomus Regius: Calcified Cartilage and not Bone as the Primary Site of Mgp Accumulation in Fish Authors: Simes, D.C. / Williamson, M.K. / Ortiz-Delgado, J.B. / Viegas, C.S. / Price, P.A. / Cancela, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vzm.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vzm.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vzm_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 1vzm_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 1vzm_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1vzm_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vzm ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vzm | 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein/peptide | Mass: 5046.506 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ARGYROSOMUS REGIUS (meagre) / References: UniProt: Q800Y1 #2: Chemical | ChemComp-MG / #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: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 294 K / pH: 8.5 Details: DROPS OF 1.5 MICRO-L OF PROTEIN SOLUTION, 10 MG/ML OSTEOCALCIN, 5 MM CACL2 AND 30 MM TRIS-HCL PH = 8, PLUS 1.5 MICRO-L OF WELL SOLUTION, MGCL2 0.2M, 30% PEG 4K AND TRIS-HCL 0.1M PH = 8.5, ...Details: DROPS OF 1.5 MICRO-L OF PROTEIN SOLUTION, 10 MG/ML OSTEOCALCIN, 5 MM CACL2 AND 30 MM TRIS-HCL PH = 8, PLUS 1.5 MICRO-L OF WELL SOLUTION, MGCL2 0.2M, 30% PEG 4K AND TRIS-HCL 0.1M PH = 8.5, WERE EQUILIBRATED AGAINST 500 ML OF WELL SOLUTION AT 21DEGREES C OVER 2-3 WEEKS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.75 Å / Num. obs: 32430 / % possible obs: 98.5 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.2 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.4→39.75 Å / Num. parameters: 11214 / Num. restraintsaints: 13702 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: EQUIVALENT BOND DISTANCES BETWEEN MAGNESIUM AND WATER-OXYGENS OR CARBOXYLATE-OXYGENS, WERE RESTRAINED TO CORRESPONDING AVERAGE DISTANCES, WITHOUT SPECIFIC TARGET VALUES 17 RESIDUES WERE ...Details: EQUIVALENT BOND DISTANCES BETWEEN MAGNESIUM AND WATER-OXYGENS OR CARBOXYLATE-OXYGENS, WERE RESTRAINED TO CORRESPONDING AVERAGE DISTANCES, WITHOUT SPECIFIC TARGET VALUES 17 RESIDUES WERE MODELED WITH ALTERNATING SIDE-CHAINS, AND 5 RESIDUES HAVE THEIR SIDE-CHAINS NOT TOTALLY INSIDE 1 SIGMA (0.07 ELECTRONS/A**3) ELECTRON DENSITY MAPS
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 811 / Occupancy sum non hydrogen: 1193.75 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→39.75 Å
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Refine LS restraints |
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