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- PDB-4j68: Crystal structure of Ribonuclease A soaked in 40% Isopropanol: On... -

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Basic information

Entry
Database: PDB / ID: 4j68
TitleCrystal structure of Ribonuclease A soaked in 40% Isopropanol: One of twelve in MSCS set
ComponentsRibonuclease pancreaticPancreatic ribonuclease family
KeywordsHYDROLASE / Endoribonuclease
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.779 Å
AuthorsKearney, B.M. / Dechene, M. / Swartz, P.D. / Mattos, C.
CitationJournal: to be published
Title: DRoP: A program for analysis of water structure on protein surfaces
Authors: Kearney, B.M. / Roberts, D. / Dechene, M. / Swartz, P.D. / Mattos, C.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)13,9855
Polymers13,7081
Non-polymers2764
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.478, 63.478, 64.227
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-340-

HOH

21A-365-

HOH

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Components

#1: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


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


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35% ammonium sulfate, 1.5 M sodium chloride, 35 mg/mL protein in 20 mM sodium phosphate buffer, pH 6.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2004 / Details: mirror
RadiationMonochromator: Double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.779→50 Å / Num. all: 14778 / Num. obs: 14778 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.076 / Χ2: 1.365 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.78-1.84100.78714480.8191100
1.84-1.92110.53314530.8551100
1.92-2110.35314510.8681100
2-2.11110.23914540.91100
2.11-2.24110.17214660.9461100
2.24-2.42110.12414550.9861100
2.42-2.66110.09914831.0611100
2.66-3.0410.90.07214911.2441100
3.04-3.8310.90.0514902.7911100
3.83-509.80.03915873.192199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPH

1rph


Resolution: 1.779→41.764 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1484 10.06 %RANDOM
Rwork0.1816 ---
all0.1842 14755 --
obs0.1842 14753 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.08 Å2 / Biso mean: 28.537 Å2 / Biso min: 15.27 Å2
Refinement stepCycle: LAST / Resolution: 1.779→41.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 17 86 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007984
X-RAY DIFFRACTIONf_angle_d1.1691321
X-RAY DIFFRACTIONf_chiral_restr0.077145
X-RAY DIFFRACTIONf_plane_restr0.006172
X-RAY DIFFRACTIONf_dihedral_angle_d12.969358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7794-1.83680.22851360.220511811317
1.8368-1.90250.2581320.198511761308
1.9025-1.97860.20691300.185311911321
1.9786-2.06870.21761340.179511911325
2.0687-2.17770.1951360.165311881324
2.1777-2.31420.24751370.171412021339
2.3142-2.49280.20421320.184212041336
2.4928-2.74360.21471320.185312081340
2.7436-3.14050.20041340.187612051339
3.1405-3.95630.18051370.162112301367
3.9563-41.77560.21341440.192112931437

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