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- PDB-1c9v: H12A VARIANT OF RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 1c9v
TitleH12A VARIANT OF RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / ANTIPARALLEL BETA SHEET
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 / Resolution: 1.7 Å
AuthorsPark, C. / Schultz, L.W. / Raines, R.T.
CitationJournal: Biochemistry / Year: 2001
Title: Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding.
Authors: Park, C. / Schultz, L.W. / Raines, R.T.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7123
Polymers13,6411
Non-polymers712
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.540, 64.540, 65.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBONUCLEASE A


Mass: 13641.257 Da / Num. of mol.: 1 / Mutation: H12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: PANCREAS / Plasmid: PET22B+ / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% ammonium sulfate, 50% sodium chloride, 100mM sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.050 Msodium acetate1drop
233 mg/mlprotein1drop
325 %(v/v)sat1dropNaCl
415 %(v/v)satammonium sulfate1drop
50.10 Msodium acetate1reservoir
650 %(v/v)1reservoirNaCl
730 %(v/v)satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 20142 / % possible obs: 96 % / Observed criterion σ(I): 0.33 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.13 / % possible all: 88
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0.33 / Redundancy: 2.5 % / Num. measured all: 50643 / Rmerge(I) obs: 0.03 / Biso Wilson estimate: 0 Å2
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 88 %

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Processing

Software
NameClassification
FRAMBOdata collection
XDSdata reduction
TNTrefinement
XDSdata scaling
TNTphasing
RefinementResolution: 1.7→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.182 20981 -
obs-20142 96 %
Solvent computationBsol: 289.8 Å2 / ksol: 0.943 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 2 98 1060
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_incorr_chiral_ct00
X-RAY DIFFRACTIONt_angle_deg2.41130513
X-RAY DIFFRACTIONt_bond_d0.01196510
X-RAY DIFFRACTIONt_trig_c_planes0.012825
X-RAY DIFFRACTIONt_gen_planes0.01313950
X-RAY DIFFRACTIONt_dihedral_angle_d17.9195870
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0125
X-RAY DIFFRACTIONt_plane_restr0.01350
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.9190

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