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- PDB-4wyn: The crystal structure of the A109G mutant of RNase A -

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Basic information

Entry
Database: PDB / ID: 4wyn
TitleThe crystal structure of the A109G mutant of RNase A
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / conformational dynamics
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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsFrench, R.L. / Gagne, D. / Doucet, N. / Simonovic, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105978 United States
CitationJournal: Structure / Year: 2015
Title: Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity.
Authors: Gagne, D. / French, R.L. / Narayanan, C. / Simonovic, M. / Agarwal, P.K. / Doucet, N.
History
DepositionNov 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Jun 1, 2016Group: Data collection
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)27,6512
Polymers27,6512
Non-polymers00
Water6,882382
1
A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,8251
Polymers13,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,8251
Polymers13,8251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.174, 51.435, 58.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 13825.496 Da / Num. of mol.: 2 / Mutation: A109G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RNASE1, RNS1 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB buffer, 20% (w/v) PEG 1,500 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.987 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21263 / % possible obs: 98.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.096 / Rrim(I) all: 0.212 / Χ2: 1.388 / Net I/av σ(I): 8.696 / Net I/σ(I): 13.6 / Num. measured all: 83203
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.10.289500.8790.2170.3570.94190.6
1.83-1.862.40.2749890.8840.2010.3420.96293.5
1.86-1.93.10.27710330.8860.1820.3341.32898.2
1.9-1.943.30.25610390.9190.1590.3031.10498.7
1.94-1.983.50.23910380.9130.1470.2821.2598.9
1.98-2.033.60.22810600.8790.1380.2681.22299.5
2.03-2.083.70.22110570.9150.1270.2561.54499.8
2.08-2.133.90.19610610.9470.1120.2271.13199.8
2.13-2.23.90.19110470.9520.1070.221.151100
2.2-2.274.10.210620.9280.110.2291.544100
2.27-2.354.20.17910750.9640.0960.2041.252100
2.35-2.444.30.17410660.9670.0910.1971.263100
2.44-2.554.30.16610670.970.0850.1871.523100
2.55-2.694.40.16310770.950.0840.1841.313100
2.69-2.864.50.17510770.9580.0860.1961.64100
2.86-3.084.50.17110830.9370.0860.1921.556100
3.08-3.394.60.16310910.9660.080.1821.517100
3.39-3.884.50.16510970.9440.0820.1851.557100
3.88-4.884.50.20211110.9310.10.2261.50399.6
4.88-504.20.21711830.9040.1120.2451.58198.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.805→34.394 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 1081 5.11 %Random selection
Rwork0.1456 20065 --
obs0.1484 21146 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.43 Å2 / Biso mean: 19.1313 Å2 / Biso min: 3.17 Å2
Refinement stepCycle: final / Resolution: 1.805→34.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 0 382 2252
Biso mean---29.3 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111972
X-RAY DIFFRACTIONf_angle_d1.2932674
X-RAY DIFFRACTIONf_chiral_restr0.051302
X-RAY DIFFRACTIONf_plane_restr0.006354
X-RAY DIFFRACTIONf_dihedral_angle_d13.399730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.805-1.88750.26391120.18112281239391
1.8875-1.9870.2191560.15652485264199
1.987-2.11150.22411280.14242504263299
2.1115-2.27450.20591220.13882529265199
2.2745-2.50330.18361370.14452545268299
2.5033-2.86540.22791500.14622527267799
2.8654-3.60940.20631370.13712560269799
3.6094-34.40030.17461390.14632634277397

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