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- PDB-4n4c: Crystal structure of the C-terminal swapped dimer of a Bovine sem... -

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Basic information

Entry
Database: PDB / ID: 4n4c
TitleCrystal structure of the C-terminal swapped dimer of a Bovine seminal ribonuclease mutant
ComponentsSeminal ribonuclease
KeywordsHYDROLASE / C-TERMINAL DOMAIN SWAPPING / RIBONUCLEASE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / metabolic process / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
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
PHOSPHATE ION / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsPica, A. / Russo Krauss, I. / Merlino, A. / Sica, F.
CitationJournal: Febs Lett. / Year: 2013
Title: The multiple forms of bovine seminal ribonuclease: Structure and stability of a C-terminal swapped dimer.
Authors: Sica, F. / Pica, A. / Merlino, A. / Russo Krauss, I. / Ercole, C. / Picone, D.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Seminal ribonuclease
B: Seminal ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6334
Polymers27,4432
Non-polymers1902
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-41 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.802, 79.044, 75.379
Angle α, β, γ (deg.)90.00, 101.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Seminal ribonuclease / S-RNase / Seminal RNase / Ribonuclease BS-1


Mass: 13721.732 Da / Num. of mol.: 2 / Fragment: UNP residues 27-150 / Mutation: G16S, N17T, P19A, S20A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SRN / Production host: Escherichia coli (E. coli) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 16-20% w/v PEG35K, 0.2 M lithium chloride, 0.1 M sodium cacodylate buffer, pH 6.0, 3% v/v acetonitrile, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0099 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0099 Å / Relative weight: 1
Reflection twinOperator: H,-K,-H-L / Fraction: 0.49
ReflectionResolution: 2.48→19.761 Å / Num. all: 12037 / Num. obs: 9497 / % possible obs: 78.9 %
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 2 % / Num. unique all: 467 / % possible all: 39

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1X

1n1x


Resolution: 2.48→19.761 Å / σ(F): 1.42 / Phase error: 18.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 420 4.77 %RANDOM
Rwork0.1697 ---
obs0.171 8805 74.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→19.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 10 35 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091983
X-RAY DIFFRACTIONf_angle_d1.2892658
X-RAY DIFFRACTIONf_dihedral_angle_d14.551757
X-RAY DIFFRACTIONf_chiral_restr0.048294
X-RAY DIFFRACTIONf_plane_restr0.009341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.84140.2537850.19711671X-RAY DIFFRACTION43
2.8414-3.57640.21711370.16022940X-RAY DIFFRACTION75
3.5764-19.76160.15891890.16393762X-RAY DIFFRACTION95

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