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Yorodumi- PDB-3zlb: Crystal structure of phosphoglycerate kinase from Streptococcus p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zlb | ||||||
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Title | Crystal structure of phosphoglycerate kinase from Streptococcus pneumoniae | ||||||
Components | PHOSPHOGLYCERATE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information phosphoglycerate kinase / phosphoglycerate kinase activity / positive regulation of plasminogen activation / angiostatin binding / positive regulation of fibrinolysis / peptidoglycan-based cell wall / glycolytic process / protease binding / cell surface / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Bernardo-Garcia, N. / Hermoso, J.A. | ||||||
Citation | Journal: Thromb. Haemost. / Year: 2014 Title: Pneumococcal phosphoglycerate kinase interacts with plasminogen and its tissue activator. Authors: Fulde, M. / Bernardo-Garcia, N. / Rohde, M. / Nachtigall, N. / Frank, R. / Preissner, K.T. / Klett, J. / Morreale, A. / Chhatwal, G.S. / Hermoso, J.A. / Bergmann, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zlb.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zlb.ent.gz | 198.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zlb_validation.pdf.gz | 750 KB | Display | wwPDB validaton report |
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Full document | 3zlb_full_validation.pdf.gz | 753.3 KB | Display | |
Data in XML | 3zlb_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3zlb_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zlb ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zlb | HTTPS FTP |
-Related structure data
Related structure data | 1vpeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41985.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: D39 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: Q04LZ5, phosphoglycerate kinase | ||||||
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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ANP / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→46.93 Å / Num. obs: 34968 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VPE Resolution: 1.78→46.937 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→46.937 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.0032 Å / Origin y: -12.9341 Å / Origin z: -12.4408 Å
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Refinement TLS group | Selection details: ALL |