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- PDB-4j64: Crystal structure of Ribonuclease A soaked in 40% Dioxane: One of... -

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Basic information

Entry
Database: PDB / ID: 4j64
TitleCrystal structure of Ribonuclease A soaked in 40% Dioxane: 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 / defense response to Gram-positive bacterium / lyase activity / 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
1,4-DIETHYLENE DIOXIDE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.781 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1576
Polymers13,7081
Non-polymers4485
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.545, 63.545, 63.898
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 (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
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: 1.78→50 Å / Num. all: 14694 / Num. obs: 14694 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.083 / Χ2: 1.294 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.78-1.8410.30.65614440.8391100
1.84-1.92110.47614560.8611100
1.92-2110.31814330.9241100
2-2.11110.22114410.9441100
2.11-2.24110.16514540.9541100
2.24-2.42110.12414501.0261100
2.42-2.66110.09714771.0351100
2.66-3.04110.06914771.1051100
3.04-3.8310.10.04914841.489199.7
3.83-5010.20.04615783.7561100

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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: 1.781→41.699 Å / Occupancy max: 1 / Occupancy min: 0.09 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1460 9.95 %RANDOM
Rwork0.1775 ---
all0.1807 14678 --
obs0.1807 14668 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.4 Å2 / Biso mean: 24.0351 Å2 / Biso min: 10.44 Å2
Refinement stepCycle: LAST / Resolution: 1.781→41.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 29 90 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007999
X-RAY DIFFRACTIONf_angle_d1.3381336
X-RAY DIFFRACTIONf_chiral_restr0.09145
X-RAY DIFFRACTIONf_plane_restr0.006172
X-RAY DIFFRACTIONf_dihedral_angle_d18.748382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.781-1.84460.21891440.199312991443
1.8446-1.91850.21211420.188813091451
1.9185-2.00580.21441420.178412961438
2.0058-2.11150.21071400.168312981438
2.1115-2.24380.19731480.169313061454
2.2438-2.4170.2021400.171413051445
2.417-2.66020.22421460.182913311477
2.6602-3.04510.19191500.184513251475
3.0451-3.83610.2171480.16313351483
3.8361-41.710.20921600.185214041564

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