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Yorodumi- PDB-1qhc: CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-PHOSPHO-2'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qhc | ||||||
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Title | CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-PHOSPHO-2'-DEOXYURIDINE-3'-PYROPHOSPHATE ADENOSINE-3'-PHOSPHATE | ||||||
Components | PROTEIN (RIBONUCLEASE A) | ||||||
Keywords | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Leonidas, D.D. / Acharya, K.R. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Toward rational design of ribonuclease inhibitors: high-resolution crystal structure of a ribonuclease A complex with a potent 3',5'-pyrophosphate-linked dinucleotide inhibitor. Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R. #1: Journal: Biochemistry / Year: 1997 Title: Crystal Structures of Ribonuclease A Complexes with 5'-Diphosphoadenosine 3'- Phosphate and 5'-Diphosphoadenosine 2'-Phosphate at 1.7 A Resolution Authors: Leonidas, D.D. / Shapiro, R. / Irons, L.I. / Russo, N. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qhc.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qhc.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qhc_validation.pdf.gz | 503.2 KB | Display | wwPDB validaton report |
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Full document | 1qhc_full_validation.pdf.gz | 508.6 KB | Display | |
Data in XML | 1qhc_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1qhc_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qhc ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qhc | HTTPS FTP |
-Related structure data
Related structure data | 1afkS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.574776, 0.784184, 0.233854), Vector: |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | Y | Sequence details | 1AFK A SWS P00656 1 - 26 NOT IN ATOMS LIST 1AFK B SWS P00656 1 - 26 NOT IN ATOMS LIST | |
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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: 2.2 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: CRYSTALLIZED FROM 20% PEG 4000, 20 MM SODIUM CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Details: Leonidas, D.D., (1997) Biochemistry, 36, 5578. | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 25723 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.05 / Rsym value: 0.326 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFK Resolution: 1.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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Displacement parameters | Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.386 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.374 |