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- PDB-1eid: CRYSTAL STRUCTURE OF F120G MUTANT OF BOVINE PANCREATIC RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 1eid
TitleCRYSTAL STRUCTURE OF F120G MUTANT OF 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 / 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
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
DepositionFeb 25, 2000Deposition site: RCSB / Processing site: RCSB
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 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)13,6181
Polymers13,6181
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.733, 63.733, 63.490
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


Mass: 13618.204 Da / Num. of mol.: 1 / Mutation: F120G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: 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.: 142 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
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
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH6.0
330 %(v/v)saturatedammonium sulfate1reservoir
450 %(v/v)saturated1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.708459
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708459 Å / Relative weight: 1
ReflectionResolution: 1.2→41.655 Å / Num. all: 47039 / Num. obs: 41727 / % possible obs: 88.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.6
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5 % / Rmerge(I) obs: 0.307 / Num. unique all: 4032 / % possible all: 87.3
Reflection
*PLUS
Lowest resolution: 41.7 Å / Num. measured all: 404905

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.4→5.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 118515.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2613 10 %RANDOM
Rwork0.21 ---
all-26197 --
obs-26197 89.2 %-
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.18 Å20 Å2
2--0.41 Å20 Å2
3----0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-6 Å
Luzzati sigma a0.02 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.4→5.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 142 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 267 10.4 %
Rwork0.259 2309 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.57
X-RAY DIFFRACTIONx_mcbond_it1.431.5
X-RAY DIFFRACTIONx_scbond_it2.152
X-RAY DIFFRACTIONx_mcangle_it2.472
X-RAY DIFFRACTIONx_scangle_it3.262.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.259

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