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- PDB-2blp: RNase before unattenuated X-RAY burn -

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Basic information

Entry
Database: PDB / ID: 2blp
TitleRNase before unattenuated X-RAY burn
ComponentsRIBONUCLEASE PANCREATIC PRECURSOR
KeywordsHYDROLASE / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA phosphodiester bond hydrolysis / ribonuclease activity / nucleic acid binding / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease family signature. / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsNanao, M.H. / Ravelli, R.B.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Improving radiation-damage substructures for RIP.
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.
History
DepositionMar 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol
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

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Assembly

Deposited unit
A: RIBONUCLEASE PANCREATIC PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7442
Polymers13,7081
Non-polymers351
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.132, 64.132, 63.643
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2121-

HOH

21A-2143-

HOH

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Components

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


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDONUCLEASE THAT CATALYZES THE CLEAVAGE OF RNA ON THE 3' SIDE OF PYRIMIDINE NUCLEOTIDES. ACTS ON ...ENDONUCLEASE THAT CATALYZES THE CLEAVAGE OF RNA ON THE 3' SIDE OF PYRIMIDINE NUCLEOTIDES. ACTS ON SINGLE STRANDED AND DOUBLE STRANDED RNA.

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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: 2.79 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 5.5
Details: 30 % PEG 5000 MME,1 M SODIUM CHLORIDE,50 MM PH 4.5 SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939255
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939255 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 55873 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.93
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.25 / % possible all: 90.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.414 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES LYS 1,LYS 31,LYS 37,ASP ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES LYS 1,LYS 31,LYS 37,ASP 38,ARG 39,LYS 91, LYS 104
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1509 5.1 %RANDOM
Rwork0.145 ---
obs0.147 28316 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 1 143 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021975
X-RAY DIFFRACTIONr_bond_other_d0.0020.02809
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9251321
X-RAY DIFFRACTIONr_angle_other_deg0.99231913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56225.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19415169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.121154
X-RAY DIFFRACTIONr_chiral_restr0.110.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_nbd_refined0.3190.2172
X-RAY DIFFRACTIONr_nbd_other0.2320.2779
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2486
X-RAY DIFFRACTIONr_nbtor_other0.0890.2560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5320.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1411.5791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.68421010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4853407
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5324.5310
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.48 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.22 210
Rwork0.158 4019

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