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Yorodumi- PDB-1kp0: The Crystal Structure Analysis of Creatine Amidinohydrolase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kp0 | ||||||
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Title | The Crystal Structure Analysis of Creatine Amidinohydrolase from Actinobacillus | ||||||
Components | CREATINE AMIDINOHYDROLASE | ||||||
Keywords | HYDROLASE / Alpha Betal / 3-Layer(aba) Sandwich | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Actinobacillus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Padmanabhan, B. / Paehler, A. / Horikoshi, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of creatine amidinohydrolase from Actinobacillus. Authors: Padmanabhan, B. / Paehler, A. / Horikoshi, M. | ||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. ...sequence an appropriate sequence database reference was not available at the time of processing. the authors state that the sequence was derived from the crystal structure. AT THE END OF FINAL REFINEMENT, RESIDUES (ASP,ASN,GLU, AND GLN) WHICH ARE CONSERVED BETWEEN P.PUTIDA AND BACILLUS CREATINASE WERE TREATED AS THE SAME CORRESPONDING RESIDUES AT EQUIVALENT POSITIONS IN AC.BACILLUS CREATINASE OR OTHERWISE TREATED AS ASX OR GLX. GLX: 5,7,13,21,28,68,72,119,134,136,149,154,163,168 GLX: 204,240,267,268,275,278,289,310,345 ASX: 29,39,71,94,130,164,199,208,236,270,306,329,362,384 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kp0.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kp0.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kp0_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 1kp0_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 1kp0_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 1kp0_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/1kp0 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/1kp0 | HTTPS FTP |
-Related structure data
Related structure data | 1chmS 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: 44726.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Actinobacillus (bacteria) / Genus: Actinobacillus / References: UniProt: Q7SIB5, creatinase #2: Water | ChemComp-HOH / | Has protein modification | N | |
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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: 3.26 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 33916 / Num. obs: 33902 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 167670 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.151 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1CHM Resolution: 2.7→30 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 13.5746 Å2 / ksol: 0.310792 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.191 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.321 / Rfactor Rwork: 0.26 |