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- PDB-5d97: Neutron crystal structure of H2O-solvent ribonuclease A -

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Basic information

Entry
Database: PDB / ID: 5d97
TitleNeutron crystal structure of H2O-solvent ribonuclease A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Ribonuclease A / D/H contrast
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
ISOPROPYL ALCOHOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.8 Å
AuthorsChatake, T. / Fujiwara, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI23770176 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography
Authors: Chatake, T. / Fujiwara, S.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 5, 2018Group: Data collection / Refinement description
Category: refine / refine_hist ...refine / refine_hist / refine_ls_restr / refine_ls_shell
Item: _refine.pdbx_refine_id / _refine_hist.pdbx_refine_id ..._refine.pdbx_refine_id / _refine_hist.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7682
Polymers13,7081
Non-polymers601
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area6980 Å2
Unit cell
Length a, b, c (Å)30.340, 38.369, 53.188
Angle α, β, γ (deg.)90.00, 105.75, 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 / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.41 % / Description: H2O-solvent crystal of ribonuclease A
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 5.8
Details: 20 mg/mL ribonuclease A, 0.05 M sodium acetate, 50% 2-propanol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 16, 2010 / Details: The BIX-3 neutron diffractometer at JRR-3M of JAEA
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.9 Å / Relative weight: 1
ReflectionResolution: 1.8→30.7 Å / Num. obs: 7979 / % possible obs: 72.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 5.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.9 / % possible all: 48.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496model building
DENZOdata processing
SCALEPACKdata reduction
CNSphasing
PHENIX1.8.4_1496refinement
RefinementResolution: 1.8→30.7 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 401 5.03 %
Rwork0.2202 --
obs0.2204 7979 72.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 4 107 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0891928
NEUTRON DIFFRACTIONf_angle_d13346
NEUTRON DIFFRACTIONf_dihedral_angle_d16.486497
NEUTRON DIFFRACTIONf_chiral_restr0.054148
NEUTRON DIFFRACTIONf_plane_restr0.006303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-2.06050.30361050.30941948NEUTRON DIFFRACTION56
2.0605-2.59590.21451210.22542464NEUTRON DIFFRACTION71
2.5959-30.70660.1881750.17753166NEUTRON DIFFRACTION89

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