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Yorodumi- PDB-4b6z: Crystal structure of metallo-carboxypeptidase from Burkholderia c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b6z | ||||||
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Title | Crystal structure of metallo-carboxypeptidase from Burkholderia cenocepacia | ||||||
Components | FAMILY M14 UNASSIGNED PEPTIDASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BURKHOLDERIA CENOCEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rimsa, V. / Eadsforth, T.C. / Joosten, R.P. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: High-Resolution Structure of the M14-Type Cytosolic Carboxypeptidase from Burkholderia Cenocepacia Refined Exploiting Pdb_Redo Strategies. Authors: Rimsa, V. / Eadsforth, T.C. / Joosten, R.P. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b6z.cif.gz | 620.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b6z.ent.gz | 515.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b6z_validation.pdf.gz | 515.6 KB | Display | wwPDB validaton report |
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Full document | 4b6z_full_validation.pdf.gz | 531.1 KB | Display | |
Data in XML | 4b6z_validation.xml.gz | 65.8 KB | Display | |
Data in CIF | 4b6z_validation.cif.gz | 94.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b6z ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b6z | HTTPS FTP |
-Related structure data
Related structure data | 3k2kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45196.402 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ZINC IS COORDINATED BY H171, E174, H268 / Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / LMG 16656 / Plasmid: PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4EEQ5 |
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-Non-polymers , 7 types, 1077 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-PEG / | #8: 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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | Details: 100 NL OF PROTEIN SOLUTION (10 MG ML-1 IN 100 MM SODIUM ACETATE PH 5.0, 150 MM NACL AND 0.5 MM ZINC SULPHATE) WERE MIXED AT 1:1 RATIO WITH RESERVOIR (0.2M LITHIUM SULPHATE, 25% PEG 3350 AND ...Details: 100 NL OF PROTEIN SOLUTION (10 MG ML-1 IN 100 MM SODIUM ACETATE PH 5.0, 150 MM NACL AND 0.5 MM ZINC SULPHATE) WERE MIXED AT 1:1 RATIO WITH RESERVOIR (0.2M LITHIUM SULPHATE, 25% PEG 3350 AND 0.1M BIS-TRIS, PH 5.5) EQUILIBRATED AGAINST A 70 UL RESERVOIR. CRYSTALS WERE OBSERVED AFTER THREE DAYS. |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 17, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 124234 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3K2K Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.009 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. RESIDUE 1 IN CHAINS A,B AND C. RESIDUES 157-158 IN CHAINS A,C. RESIDUE 319 IN CHAIN B, RESIDUES 315- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. RESIDUE 1 IN CHAINS A,B AND C. RESIDUES 157-158 IN CHAINS A,C. RESIDUE 319 IN CHAIN B, RESIDUES 315-319 IN CHAIN C, RESIDUES 316-319 IN CHAIN D. RESIDUES 384 IN CHAIN A.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.436 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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