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- PDB-1w4p: Binding of Nonnatural 3'-Nucleotides to Ribonuclease A -

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Basic information

Entry
Database: PDB / ID: 1w4p
TitleBinding of Nonnatural 3'-Nucleotides to Ribonuclease A
ComponentsPANCREATIC RIBONUCLEASE A
KeywordsHYDROLASE / NONNATURAL 3'-NUCLEOTIDES / RNASE A / RIBONUCLEASE / ENDONUCLEASE
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
2'-DEOXYURIDINE 3'-MONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsJenkins, C.L. / Thiyagarajan, N. / Sweeney, R.Y. / Guy, M.P. / Kelemen, B.R. / Acharya, K.R. / Raines, R.T.
CitationJournal: FEBS J. / Year: 2005
Title: Binding of Non-Natural 3'-Nucleotides to Ribonuclease A
Authors: Jenkins, C.L. / Thiyagarajan, N. / Sweeney, R.Y. / Guy, M.P. / Kelemen, B.R. / Acharya, K.R. / Raines, R.T.
History
DepositionJul 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PANCREATIC RIBONUCLEASE A
B: PANCREATIC RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0334
Polymers27,4172
Non-polymers6162
Water5,224290
1
A: PANCREATIC RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0172
Polymers13,7081
Non-polymers3081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PANCREATIC RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0172
Polymers13,7081
Non-polymers3081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.451, 32.942, 73.094
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PANCREATIC RIBONUCLEASE A / RNASE 1 / RNASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 2'-DEOXYURIDINE 3'-PHOSPHATE / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-UM3 / 2'-DEOXYURIDINE 3'-MONOPHOSPHATE / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.03 Å3/Da / Density % sol: 35.75 %
Crystal growpH: 5.5
Details: 20MM SODIUM CITRATE BUFFER, PH5.5, CONTAINING PEG4000 (25% W/V), pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 27984 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 8.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFU

1afu


Resolution: 1.69→41.39 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 391863.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1194 4.8 %RANDOM
Rwork0.217 ---
obs0.217 24768 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7361 Å2 / ksol: 0.39138 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--0.79 Å20 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.69→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 40 290 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.69→1.8 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 216 4.9 %
Rwork0.218 4171 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3UMP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMUMP.TOP

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