+Open data
-Basic information
Entry | Database: PDB / ID: 1cfz | ||||||
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Title | HYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI | ||||||
Components | HYDROGENASE 2 MATURATION PROTEASE | ||||||
Keywords | HYDROGENASE / MATURATION / METZINCINS / NICKEL / PROTEASE | ||||||
Function / homology | Function and homology information protein modification process => GO:0036211 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / enzyme activator activity / protein processing / endopeptidase activity / aspartic-type endopeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å | ||||||
Authors | Fritsche, E. / Paschos, A. / Beisel, H.-G. / Boeck, A. / Huber, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli. Authors: Fritsche, E. / Paschos, A. / Beisel, H.G. / Bock, A. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cfz.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cfz.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 1cfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cfz_validation.pdf.gz | 400.5 KB | Display | wwPDB validaton report |
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Full document | 1cfz_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 1cfz_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1cfz_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/1cfz ftp://data.pdbj.org/pub/pdb/validation_reports/cf/1cfz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17490.318 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P37182, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | Nonpolymer details | METAL ION WAS MODELED AS A CADMIUM ION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.91 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.099 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.099 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 62671 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 10.3 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Num. measured all: 125012 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.27 Å / % possible obs: 90.3 % / Rmerge(I) obs: 0.267 |
-Processing
Software | Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SIRAS / Resolution: 2.2→15 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. reflection Rfree: 6246 / Rfactor obs: 0.224 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |