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- PDB-3a1r: Neutron crystal structure analysis of bovine pancreatic ribonuclease A -

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Basic information

Entry
Database: PDB / ID: 3a1r
TitleNeutron crystal structure analysis of bovine pancreatic ribonuclease A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Bovine pancreatic ribonuclease A / Neutron structure / Endonuclease / glycation / Glycoprotein / Secreted / Disulfide bond / Nuclease
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
DEUTERATED WATER / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYagi, D. / Tanaka, I. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 A resolution
Authors: Yagi, D. / Yamada, T. / Kurihara, K. / Ohnishi, Y. / Yamashita, M. / Tamada, T. / Tanaka, I. / Kuroki, R. / Niimura, N.
History
DepositionApr 21, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Jul 18, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_scattering_type
Revision 1.5Nov 1, 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


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.380, 38.558, 53.398
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreas / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / pH: 6.2
Details: 50% tert-butyl alcohol, temperature 298K, then the crystal was soaked in heavy water solution, PH6.2, for two months, BATCH

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-B / Wavelength: 2.6 / Wavelength: 2.6 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 22, 2005
RadiationMonochromator: ELLASTICALLY BENT SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 1.4→80 Å / Num. all: 15039 / Num. obs: 15039 / % possible obs: 64 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.4
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.07 / % possible all: 19.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KF4

1kf4


Resolution: 1.7→30.84 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 666500.05 / Data cutoff low absF: 0 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.238 750 5 %RANDOM
Rwork0.195 ---
obs0.195 15029 63.9 %-
all-15029 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 13 Å2 / ksol: 0.06 e/Å3
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å2-0.32 Å2
2---0.25 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 92 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 50 5.4 %
Rwork0.333 870 -
obs-870 23.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PRO3.paramPRO2.top
X-RAY DIFFRACTION2SOL.paramSOL.top

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