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- PDB-4j61: Crystal structure of Ribonuclease A soaked in 40% Cyclopentanone:... -

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Basic information

Entry
Database: PDB / ID: 4j61
TitleCrystal structure of Ribonuclease A soaked in 40% Cyclopentanone: One of twelve in MSCS set
ComponentsRibonuclease pancreatic
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
cyclopentanone / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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)14,1416
Polymers13,7081
Non-polymers4335
Water1,838102
1
A: Ribonuclease pancreatic
hetero molecules

A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,28212
Polymers27,4172
Non-polymers86510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2560 Å2
ΔGint-36 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.462, 63.462, 63.927
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 / 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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MFW / cyclopentanone


Mass: 84.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
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: 1.69→50 Å / Num. all: 17106 / Num. obs: 17106 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.076 / Χ2: 1.349 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.69-1.7510.10.60616620.8551100
1.75-1.8210.80.46416990.9311100
1.82-1.9110.33116790.9591100
1.9-2110.20716930.9861100
2-2.13110.14516931.0671100
2.13-2.29110.10916941.1321100
2.29-2.5211.10.08717091.2651100
2.52-2.89110.06817251.481100
2.89-3.6410.20.04917311.8041100
3.64-5010.40.04918212.962199.9

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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: 1.69→41.675 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.13 / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1709 10.01 %RANDOM
Rwork0.1758 ---
all0.1776 17081 --
obs0.1776 17080 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.24 Å2 / Biso mean: 23.3661 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: LAST / Resolution: 1.69→41.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 29 102 1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007999
X-RAY DIFFRACTIONf_angle_d1.1821340
X-RAY DIFFRACTIONf_chiral_restr0.083145
X-RAY DIFFRACTIONf_plane_restr0.006172
X-RAY DIFFRACTIONf_dihedral_angle_d15.056386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6903-1.740.21311390.188512621401
1.74-1.79620.23291430.196612681411
1.7962-1.86040.23541410.182912461387
1.8604-1.93490.22571380.179112631401
1.9349-2.02290.17681420.170312651407
2.0229-2.12960.19491390.162212741413
2.1296-2.2630.21851430.168312661409
2.263-2.43770.20731380.173412851423
2.4377-2.6830.19681420.178412751417
2.683-3.07110.19951420.186712911433
3.0711-3.86890.16421480.163213031451
3.8689-41.68790.18481540.181513731527

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