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- PDB-1r3m: Crystal structure of the dimeric unswapped form of bovine seminal... -

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Basic information

Entry
Database: PDB / ID: 1r3m
TitleCrystal structure of the dimeric unswapped form of bovine seminal ribonuclease
ComponentsRibonuclease, seminal
KeywordsHYDROLASE / RIBONUCLEASE / SWAPPING / HINGE
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 / 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 family signature. / Pancreatic ribonuclease / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBerisio, R. / Sica, F. / De Lorenzo, C. / Di Fiore, A. / Piccoli, R. / Zagari, A. / Mazzarella, L.
Citation
Journal: Febs Lett. / Year: 2003
Title: Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease
Authors: Berisio, R. / Sica, F. / De Lorenzo, C. / Di Fiore, A. / Piccoli, R. / Zagari, A. / Mazzarella, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: BOVINE SEMINAL RIBONUCLEASE: STRUCTURE AT 1.9 A RESOLUTION
Authors: Mazzarella, L. / CAPASSO, S. / DE MASI, D. / DI LORENZO, G. / MATTIA, C.A. / ZAGARI, A.
#2: Journal: Proteins / Year: 2003
Title: THE UNSWAPPED CHAIN OF BOVINE SEMINAL RIBONUCLEASE: CRYSTAL STRUCTURE OF THE FREE AND LIGANDED MONOMERIC DERIVATIVE
Authors: SICA, F. / DI FIORE, A. / ZAGARI, A. / MAZZARELLA, L.
History
DepositionOct 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Nov 13, 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: Ribonuclease, seminal
B: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4554
Polymers27,2652
Non-polymers1902
Water1,820101
1
A: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,6331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7282
Polymers13,6331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.480, 57.550, 53.060
Angle α, β, γ (deg.)90.00, 116.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease, seminal / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: SEMINAL FLUID / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 101 / 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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 294 K / Method: evaporation / pH: 8.4
Details: MPD, ammonium sulfate, pH 8.4, EVAPORATION, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
228 %(v/v)MPD1reservoir
350 mMTris-HCl1reservoirpH8.4
40.1 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 1998
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 13585 / Num. obs: 13585 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 15.1 / Num. unique all: 2000 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 15 Å
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BSR

1bsr


Resolution: 2.2→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1975 -RANDOM
Rwork0.211 ---
all0.223 13585 --
obs0.221 13571 99.8 %-
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 10 101 1969
LS refinement shellResolution: 2.2→2.3 Å /
RfactorNum. reflection
Rfree0.35 167
Rwork0.31 -
obs-1460
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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