+Open data
-Basic information
Entry | Database: PDB / ID: 2x4m | ||||||
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Title | Yersinia Pestis Plasminogen Activator Pla | ||||||
Components | COAGULASE/FIBRINOLYSIN | ||||||
Keywords | HYDROLASE / OMPTIN / TRANSMEMBRANE / ASPARTYL PROTEASE / CELL OUTER MEMBRANE / PROTEASE | ||||||
Function / homology | Function and homology information plasminogen activator Pla / cell outer membrane / aspartic-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | YERSINIA PESTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Eren, E. / Murphy, M. / Goguen, J. / van den Berg, B. | ||||||
Citation | Journal: Structure / Year: 2010 Title: An Active Site Water Network in the Plasminogen Activator Pla from Yersinia Pestis Authors: Eren, E. / Murphy, M. / Goguen, J. / van den Berg, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4m.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4m.ent.gz | 196.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x4m_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 2x4m_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 2x4m_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 2x4m_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4m ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 32953.934 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PB22 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P17811, plasminogen activator Pla #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 106 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 106 TO ALA ...ENGINEERED | |
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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: 3.63 Å3/Da / Density % sol: 66.16 % / Description: NONE |
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Crystal grow | pH: 3.5 / Details: 16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.321 |
Reflection | Resolution: 2.55→40 Å / Num. obs: 56736 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.54→2.58 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.93 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→19.93 Å / σ(F): 0.08 / Phase error: 36.38 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.03 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.93 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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