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- PDB-1wbu: Fragment based lead discovery using crystallography -

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Basic information

Entry
Database: PDB / ID: 1wbu
TitleFragment based lead discovery using crystallography
ComponentsRIBONUCLEASE
KeywordsHYDROLASE / RIBONUCLEASE / INHIBITOR / ENDONUCLEASE / GLYCOPROTEIN
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
5-AMINO-1H-PYRIMIDINE-2,4-DIONE / Ribonuclease pancreatic / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsCleasby, A. / Hartshorn, M.J. / Murray, C.W. / Jhoti, H. / Tickle, I.J.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Fragment-Based Lead Discovery Using X-Ray Crystallography
Authors: Hartshorn, M.J. / Murray, C.W. / Cleasby, A. / Frederickson, M. / Tickle, I.J. / Jhoti, H.
History
DepositionNov 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE
B: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6714
Polymers27,4172
Non-polymers2542
Water3,999222
1
A: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8352
Polymers13,7081
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8352
Polymers13,7081
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.035, 32.604, 72.321
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RIBONUCLEASE / / RIBONUCLEASE A / RNASE 1 / RNASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS
References: UniProt: P61824, UniProt: P61823*PLUS, EC: 3.1.27.5
#2: Chemical ChemComp-WBU / 5-AMINO-1H-PYRIMIDINE-2,4-DIONE


Mass: 127.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MSC / Detector: CCD / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19 Å / Num. obs: 20393 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→19 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 926 4.9 %RANDOM
Rwork0.2069 ---
obs0.2069 18295 97.3 %-
Solvent computationSolvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.026 Å20 Å20.004 Å2
2---0.006 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 18 222 2142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003677
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.81583
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LIG_CNX.PARLIG_CNX.TOP

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