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- PDB-4ooh: Structure of RIBONUCLEASE A at 40C -

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Basic information

Entry
Database: PDB / ID: 4ooh
TitleStructure of RIBONUCLEASE A at 40C
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsYadav, S.P.S. / Sharma, P. / Ashish, F.N.U.
CitationJournal: To be Published
Title: Structure of RIBONUCLEASE A at 40C
Authors: Yadav, S.P.S. / Sharma, P. / Ashish, F.N.U.
History
DepositionFeb 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribonuclease pancreatic

A: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)27,4172
Polymers27,4172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area2060 Å2
ΔGint-6 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.956, 63.956, 64.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 13708.326 Da / Num. of mol.: 1 / Fragment: UNP residues27-150 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3M sodium chloride, 30% Ammonium Sulphate, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 313K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2014 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 23644 / Num. obs: 23644 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 14.7
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 10 / Num. unique all: 1158 / Rsym value: 0.134 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5RAT

5rat


Resolution: 1.89→20.996 Å / SU ML: 0.19 / σ(F): 1.38 / σ(I): 2 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 661 5.27 %
Rwork0.194 --
obs0.1955 12549 99.76 %
all-23644 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→20.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 63 1014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007972
X-RAY DIFFRACTIONf_angle_d1.1061305
X-RAY DIFFRACTIONf_dihedral_angle_d12.141357
X-RAY DIFFRACTIONf_chiral_restr0.077145
X-RAY DIFFRACTIONf_plane_restr0.005172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.889-2.0350.24471250.19282336100
2.035-2.23960.23461330.18962357100
2.2396-2.56320.27371300.21682371100
2.5632-3.22750.25851340.22042366100
3.2275-20.99770.18121390.1732245899

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