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- PDB-4wyz: The crystal structure of the A109G mutant of RNase A in complex w... -

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Basic information

Entry
Database: PDB / ID: 4wyz
TitleThe crystal structure of the A109G mutant of RNase A in complex with 3'UMP
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
3'-URIDINEMONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.449 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 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2994
Polymers27,6512
Non-polymers6482
Water10,431579
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1502
Polymers13,8251
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1502
Polymers13,8251
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.487, 51.841, 57.907
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 / Fragment: residues 27-150 / 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: Chemical ChemComp-U3P / 3'-URIDINEMONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MIB buffer, PEG 1500

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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: 1.449→50 Å / Num. obs: 39580 / % possible obs: 93.1 % / Redundancy: 4.6 % / Net I/σ(I): 52821

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.449→30.775 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1705 2007 5.04 %
Rwork0.1272 37826 -
obs0.1295 39580 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.23 Å2 / Biso mean: 18.2324 Å2 / Biso min: 2.88 Å2
Refinement stepCycle: final / Resolution: 1.449→30.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 64 585 2538
Biso mean--17.53 37.35 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012057
X-RAY DIFFRACTIONf_angle_d1.4452799
X-RAY DIFFRACTIONf_chiral_restr0.108314
X-RAY DIFFRACTIONf_plane_restr0.006367
X-RAY DIFFRACTIONf_dihedral_angle_d12.632766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.449-1.48550.31061080.23391971207971
1.4855-1.52560.23861240.20632227235180
1.5256-1.57050.22431340.17792503263790
1.5705-1.62120.22721560.15482725288198
1.6212-1.67920.20631270.140928112938100
1.6792-1.74640.20231400.133927892929100
1.7464-1.82590.17991390.128128072946100
1.8259-1.92210.20931530.125628052958100
1.9221-2.04250.16651450.115928122957100
2.0425-2.20020.13911400.106928162956100
2.2002-2.42150.14131470.108428392986100
2.4215-2.77170.15231530.110528473000100
2.7717-3.49130.13111820.111828513033100
3.4913-30.78240.16981590.126430233182100

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