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- PDB-6pvu: RNase A in complex with hexametaphosphate -

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Basic information

Entry
Database: PDB / ID: 6pvu
TitleRNase A in complex with hexametaphosphate
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsLYASE / RNase A / nucleotide / poly-phosphate
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
Chem-P0S / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsWindsor, I.W. / Sheppard, S.M. / Cummins, C.C. / Raines, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA073808 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A.
Authors: Shepard, S.M. / Windsor, I.W. / Raines, R.T. / Cummins, C.C.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,3764
Polymers27,4172
Non-polymers9602
Water4,738263
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1882
Polymers13,7081
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1882
Polymers13,7081
Non-polymers4801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.350, 32.640, 72.610
Angle α, β, γ (deg.)90.000, 90.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-353-

HOH

21B-453-

HOH

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-P0S / 2,4,6,8,10,12-hexahydroxy-2lambda~5~,4lambda~5~,6lambda~5~,8lambda~5~,10lambda~5~,12lambda~5~-cyclohexaphosphoxane-2,4,6,8,10,12-hexone


Mass: 479.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H6O18P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20 mM sodium citrate, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→29.57 Å / Num. obs: 38224 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.022 / Rrim(I) all: 0.052 / Net I/σ(I): 20.5
Reflection shellResolution: 1.49→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3454 / CC1/2: 0.857 / Rpim(I) all: 0.217 / Rrim(I) all: 0.466 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.25data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1afu

1afu


Resolution: 1.49→29.57 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2359 1993 5.2 %
Rwork0.2016 --
obs0.2033 38222 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.34 Å2 / Biso mean: 19.9 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 1.49→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 72 263 2223
Biso mean--53.76 24.05 -
Num. residues----248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.28091250.23952203X-RAY DIFFRACTION86
1.53-1.570.24331430.22252592X-RAY DIFFRACTION100
1.57-1.610.26721430.20422614X-RAY DIFFRACTION100
1.61-1.670.2211390.20662564X-RAY DIFFRACTION100
1.67-1.730.24561440.19882603X-RAY DIFFRACTION100
1.73-1.80.2241400.19752606X-RAY DIFFRACTION100
1.8-1.880.22941480.20052590X-RAY DIFFRACTION100
1.88-1.980.23891350.20062589X-RAY DIFFRACTION100
1.98-2.10.21561450.19312614X-RAY DIFFRACTION100
2.1-2.260.2481450.20032616X-RAY DIFFRACTION100
2.26-2.490.24221460.20892637X-RAY DIFFRACTION100
2.49-2.850.261430.20792608X-RAY DIFFRACTION100
2.85-3.590.19951500.20192659X-RAY DIFFRACTION100
3.59-29.570.24971470.19242734X-RAY DIFFRACTION100

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