+Open data
-Basic information
Entry | Database: PDB / ID: 1a2p | ||||||
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Title | BARNASE WILDTYPE STRUCTURE AT 1.5 ANGSTROMS RESOLUTION | ||||||
Components | BARNASE | ||||||
Keywords | RIBONUCLEASE / MICROBIAL RIBONUCLEASE / ALPHA/BETA PROTEIN | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Martin, C. / Richard, V. / Salem, M. / Hartley, R.W. / Mauguen, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Refinement and structural analysis of barnase at 1.5 A resolution. Authors: Martin, C. / Richard, V. / Salem, M. / Hartley, R. / Mauguen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a2p.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a2p.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a2p_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 1a2p_full_validation.pdf.gz | 424.6 KB | Display | |
Data in XML | 1a2p_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1a2p_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a2p ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a2p | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 12398.721 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PMJ1002 / Production host: Escherichia coli (E. coli) References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | #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: 2.24 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.9 Å / Num. obs: 48463 / % possible obs: 96.9 % / Redundancy: 2.5 % / Rsym value: 0.038 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.158 / % possible all: 94.5 |
Reflection | *PLUS Rmerge(I) obs: 0.038 |
-Processing
Software |
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Refinement | Resolution: 1.5→8 Å / Num. parameters: 27377 / Num. restraintsaints: 33057 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR F.GREATER THAN 3 ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR F.GREATER THAN 3 SIGMA(F), THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL-93. ANISOU RECORDS CONTAIN ANISOTROPIC DISPLACEMENT PARAMETERS U11 U22 U33 U23 U13 U12 (ANGSTROMS**2) MULTIPLIED BY 10000. ISOTROPIC EQUIVALENTS OF ANISOTROPIC TEMPERATURE FACTORS ARE ALSO PRESENTED IN THIS ENTRY.
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 2417.5 / Occupancy sum non hydrogen: 2972 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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