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- PDB-1qhc: CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-PHOSPHO-2'... -
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Open data
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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 | ||||||
![]() | PROTEIN (RIBONUCLEASE A) | ||||||
![]() | HYDROLASE / RIBONUCLEASE / ENDONUCLEASE / NUCLEOTIDE INHIBITOR | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leonidas, D.D. / Acharya, K.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.2 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.2 KB | Display | ![]() |
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Full document | ![]() | 508.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1afkS S: Starting model for refinement |
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Similar structure data |
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Links
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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: |
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Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |