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- PDB-1n3z: Crystal structure of the [S-carboxyamidomethyl-Cys31, S-carboxyam... -

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Basic information

Entry
Database: PDB / ID: 1n3z
TitleCrystal structure of the [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] monomeric derivative of the bovine seminal ribonuclease in the liganded state
ComponentsRibonuclease, seminal
KeywordsHYDROLASE / Protein-nucleotide complex
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 / 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
ADENOSINE / 3'-URIDINEMONOPHOSPHATE / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSica, F. / Di Fiore, A. / Zagari, A. / Mazzarella, L.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Bovine seminal ribonuclease: structure at 1.9 resolution
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22
Authors: Mazzarella, L. / Vitagliano, L. / Zagari, A.
#3: Journal: J.CRYST.GROWTH / Year: 1999
Title: Crystallization of multiple forms of bovine seminal ribonuclease in the liganded and unliganded state
Authors: Sica, F. / Adinolfi, S. / Berisio, R. / De Lorenzo, C. / Mazzarella, L. / Piccoli, R. / Vitagliano, L. / Zagari, A.
#4: Journal: Protein Sci. / Year: 1998
Title: Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine
Authors: Vitagliano, L. / Adinolfi, S. / Riccio, A. / Sica, F. / Zagari, A. / Mazzarella, L.
#5: Journal: Biochemistry / Year: 1998
Title: Coulombic effects of remote subsites on the active site of ribonuclease A
Authors: Fisher, B.M. / Schultz, L.W. / Raines, R.T.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease, seminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3383
Polymers13,7471
Non-polymers5912
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.69, 28.82, 67.52
Angle α, β, γ (deg.)90.0, 119.2, 90.0
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13746.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-U3P / 3'-URIDINEMONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.16 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: PEG 4000, sodium acetate, acetonitrile, glycerol (cryoprotectant), TRIS-HCl, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
228 %(w/v)PEG40001reservoir
30.1 MTris-HCl1reservoirpH8.7
40.2 Msodium acetate1reservoir
515 %(v/v)acetonitrile1reservoirpH8.8

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. all: 14570 / Num. obs: 14570 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 14.82 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 42
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 14 / Num. unique all: 723 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 99192
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1455 10 %RANDOM
Rwork0.186 ---
all0.188 14570 --
obs0.188 14330 99.9 %-
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 40 149 1125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
LS refinement shellResolution: 1.65→1.68 Å
RfactorNum. reflection% reflection
Rfree0.253 71 -
Rwork0.213 --
obs-723 99.9 %
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4

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