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- PDB-1a2w: CRYSTAL STRUCTURE OF A 3D DOMAIN-SWAPPED DIMER OF BOVINE PANCREAT... -

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Basic information

Entry
Database: PDB / ID: 1a2w
TitleCRYSTAL STRUCTURE OF A 3D DOMAIN-SWAPPED DIMER OF BOVINE PANCREATIC RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsENDONUCLEASE / RIBONUCLEASE / DOMAIN SWAPPING / HYDROLASE / PROTEIN-PROTEIN INTERACTION
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, Y. / Hart, P.J. / Schlunegger, M.P. / Eisenberg, D.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution.
Authors: Liu, Y. / Hart, P.J. / Schlunegger, M.P. / Eisenberg, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Bovine Seminal Ribonuclease: Structure at 1.9 A Resolution
Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Crystal Structure Disposition of Thymidylic Acid Tetramer in Complex with Ribonuclease A
Authors: Birdsall, D.L. / McPherson, A.
History
DepositionJan 12, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 A
B: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5845
Polymers27,4172
Non-polymers1673
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-49 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.000, 57.000, 81.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 2 / Fragment: SWAPPED HELICAL DOMAIN / Source method: isolated from a natural source
Details: SWAPPED HELICAL DOMAIN CONTAINS RESIDUES 1-15, HINGE LOOPS CONTAIN RESIDUES 16-22, MAJOR DOMAIN CONTAINS RESIDUES 23-124
Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 92 / 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: 2.7 Å3/Da / Density % sol: 61 %
Crystal growpH: 7.5
Details: 100 MM PHOSPHATE BUFFER (PH 7.5) 1.6 M AMMONIUM SULFATE 0.6 M NACL 2% PEG400
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mldimer1drop
255 mMphosphate1drop
30.05 Msodium sulfate1drop
45 mMADP1drop
50.8 Mammonium sulfate1drop
60.3 M1dropNaCl
71 %PEG4001drop
8100 mMphosphate1reservoir
91.6 Mammonium sulfate1reservoir
100.6 M1reservoirNaCl
112 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 16601 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.097 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.263 / % possible all: 92
Reflection
*PLUS
Num. measured all: 30428 / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTB

1rtb


Resolution: 2.1→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1598 9.7 %RANDOM
Rwork0.192 ---
obs0.192 16471 96.2 %-
Displacement parametersBiso mean: 20.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 3 93 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.691.5
X-RAY DIFFRACTIONx_mcangle_it1.222
X-RAY DIFFRACTIONx_scbond_it0.942
X-RAY DIFFRACTIONx_scangle_it1.552.5
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.267 197 9.16 %
Rwork0.253 1776 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION3PARAM.SO4TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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