+Open data
-Basic information
Entry | Database: PDB / ID: 4pro | ||||||
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Title | ALPHA-LYTIC PROTEASE COMPLEXED WITH PRO REGION | ||||||
Components | (ALPHA-LYTIC PROTEASE) x 2 | ||||||
Keywords | SERINE PROTEASE / PRO REGION / FOLDASE / PROTEIN FOLDING | ||||||
Function / homology | Function and homology information alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Lysobacter enzymogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure of alpha-lytic protease complexed with its pro region. Authors: Sauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pro.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pro.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pro_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 4pro_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 4pro_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 4pro_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/4pro ftp://data.pdbj.org/pub/pdb/validation_reports/pr/4pro | HTTPS FTP |
-Related structure data
Related structure data | 2proC 3proSC 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: (0.778697, 0.440619, 0.446638), Vector: |
-Components
#1: Protein | Mass: 19815.014 Da / Num. of mol.: 2 Fragment: CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION Mutation: CHAIN A, B, M158A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Fragment: CHAIN C, D / Gene: T7 / Plasmid: PT7PRO / Cellular location (production host): INCLUSION BODIES / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00778 #2: Protein | Mass: 17835.881 Da / Num. of mol.: 2 Fragment: CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION Mutation: CHAIN A, B, M158A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Fragment: CHAIN C, D / Gene: T7 / Plasmid: PT7PRO / Cellular location (production host): INCLUSION BODIES / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00778 #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: 2.87 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 7 ℃ / pH: 8 / Method: vapor diffusion / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 18, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.2 Å / Num. obs: 104427 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.4 / % possible all: 93.9 |
Reflection | *PLUS Num. obs: 31304 / Num. measured all: 104427 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PRO Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.299 / Total num. of bins used: 50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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