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- PDB-1kf3: Atomic Resolution Structure of RNase A at pH 5.9 -

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Basic information

Entry
Database: PDB / ID: 1kf3
TitleAtomic Resolution Structure of RNase A at pH 5.9
Componentspancreatic ribonuclease
KeywordsHYDROLASE / RNase A / titration / pH / crystal / soaking
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBerisio, R. / Sica, F. / Lamzin, V.S. / Wilson, K.S. / Zagari, A. / Mazzarella, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Atomic resolution structures of ribonuclease A at six pH values.
Authors: Berisio, R. / Sica, F. / Lamzin, V.S. / Wilson, K.S. / Zagari, A. / Mazzarella, L.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Protein titration in the crystal state
Authors: Berisio, R. / Lamzin, V.S. / Sica, F. / Wilson, K.S. / Zagari, A. / Mazzarella, L.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: pancreatic ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8042
Polymers13,7081
Non-polymers961
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.440, 38.380, 53.320
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein pancreatic ribonuclease / RNASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 5.9
Details: 2-propanol, pH 5.9, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method / Details: Tilton Jr., R.F., (1992) Biochemistry, 31, 2469.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein11
20.2 M11NaOH
350 %(v/v)methanol11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.05→30 Å / Num. all: 53498 / Num. obs: 53498 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.33 / Net I/σ(I): 18.9
Reflection shellResolution: 1.05→1.07 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2545 / % possible all: 92.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 53494

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7rsa

7rsa


Resolution: 1.05→30 Å / Num. parameters: 11496 / Num. restraintsaints: 14435 / Stereochemistry target values: ENGH AND HUBER
Details: Please note: ASUL 325 AND BHOH 168 ARE ALTERNATE CONFORMATIONS. CHOH 159 IS ALTERNATIVE ONLY TO THE A CONFORMER OF HIS119. CHOH 138 IS ALTERNATIVE ONLY TO THE A CONFORMER OF ASN 103.
RfactorNum. reflection% reflection
all0.102 53494 -
obs--96.7 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 893.75 / Occupancy sum non hydrogen: 1149.31
Refinement stepCycle: LAST / Resolution: 1.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 5 246 1298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.152
LS refinement shellResolution: 1.05→1.09 Å /
RfactorNum. reflection
Rwork0.134 -
obs-5478
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.152

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