+Open data
-Basic information
Entry | Database: PDB / ID: 7ecc | ||||||
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Title | M4 family peptidase PlM4P-mature form | ||||||
Components | M4 family peptidase | ||||||
Keywords | HYDROLASE / peptidase | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | Pseudoalteromonas lipolytica SCSIO 04301 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yang, J. | ||||||
Citation | Journal: To Be Published Title: M4 family peptidase PlM4P-mature form Authors: Yang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ecc.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ecc.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ecc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ecc_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 7ecc_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 7ecc_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7ecc_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ecc ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ecc | HTTPS FTP |
-Related structure data
Related structure data | 3nqxS 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: 34909.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas lipolytica SCSIO 04301 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Molecular Dimensions Morpheus II C12: 4mM Alkalis, 0.1M buffer 6, 31% precipitant mix 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 29, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→20.13 Å / Num. obs: 22253 / % possible obs: 99.8 % / Redundancy: 8.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.085 / Rrim(I) all: 0.262 / Net I/σ(I): 4.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nqx Resolution: 2→20.13 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.583 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 55.96 Å2 / Biso mean: 21.632 Å2 / Biso min: 9.17 Å2
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Refinement step | Cycle: final / Resolution: 2→20.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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