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- PDB-1c8w: THR45GLY VARIANT OF RIBONUCLEASE A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c8w
TitleTHR45GLY VARIANT OF RIBONUCLEASE A
ComponentsPROTEIN (Ribonuclease A)
KeywordsHYDROLASE / ANTI-PARALLEL BETA SHEET / RNASE A
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
ACETATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKelemen, B.R. / Sweeney, R.T. / Schultz, L.W. / Raines, R.T.
CitationJournal: Biochemistry / Year: 2000
Title: Excavating an active site: the nucleobase specificity of ribonuclease A.
Authors: Kelemen, B.R. / Schultz, L.W. / Sweeney, R.Y. / Raines, R.T.
History
DepositionJul 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: 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 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (Ribonuclease A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8305
Polymers13,6641
Non-polymers1654
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.32, 64.32, 64.84
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-245-

HOH

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Components

#1: Protein PROTEIN (Ribonuclease A)


Mass: 13664.273 Da / Num. of mol.: 1 / Fragment: RNASE A / Mutation: T45G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: pancreas / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / References: UniProt: P61823
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, sodium chloride, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.050 Msodium acetate1droppH5.6
260 mg/mlprotein1drop
315 %(w/v)ammonium sulfate1drop
425 %(w/v)1dropNaCl
50.10 Msodium acetate1reservoirpH5.6
630 %(w/v)ammonium sulfate1reservoir
750 %(w/v)1reservoirNaCl

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 8, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 18836 / Num. obs: 18761 / % possible obs: 96 % / Observed criterion σ(F): 0.33 / Observed criterion σ(I): 0.33 / Redundancy: 3.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.19 / Num. unique all: 18761 / % possible all: 87
Reflection
*PLUS
Num. measured all: 32164
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameClassification
FRAMBOdata collection
XDSdata reduction
TNTrefinement
XDSdata scaling
TNTphasing
RefinementResolution: 1.8→30 Å / σ(F): 0.33 / σ(I): 0.33
RfactorNum. reflection% reflection
Rwork0.176 --
all-19542 -
obs-18761 96 %
Solvent computationBsol: 265.25 Å2 / ksol: 0.90215 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 7 115 1090
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01110017
X-RAY DIFFRACTIONt_angle_deg2.43135810
X-RAY DIFFRACTIONt_dihedral_angle_d18.156160
X-RAY DIFFRACTIONt_trig_c_planes0.0072925
X-RAY DIFFRACTIONt_gen_planes0.01214850
X-RAY DIFFRACTIONt_nbd0.0731850
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_planar_d0.00725
X-RAY DIFFRACTIONt_plane_restr0.01250

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