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- PDB-1fs3: CRYSTAL STRUCTURE OF WILD-TYPE BOVINE PANCREATIC RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 1fs3
TitleCRYSTAL STRUCTURE OF WILD-TYPE BOVINE PANCREATIC RIBONUCLEASE A
ComponentsRibonuclease A
KeywordsHYDROLASE / ribonuclease / RNase A / Bovine pancreas
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsChatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T.
CitationJournal: Protein Sci. / Year: 2002
Title: Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 A resolution.
Authors: Chatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T.
History
DepositionSep 8, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease A


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.046, 64.046, 63.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Ribonuclease A / Ribonuclease pancreatic


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.968641
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968641 Å / Relative weight: 1
ReflectionResolution: 1.4→6 Å / Num. all: 33877 / Num. obs: 33471 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Num. unique all: 3202 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.4→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 108825.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2911 10 %RANDOM
Rwork0.217 ---
obs0.217 29108 98.3 %-
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.65 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-6 Å
Luzzati sigma a0.08 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 115 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.242 270 9.5 %
Rwork0.204 2568 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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