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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 APancreatic ribonuclease
KeywordsENDONUCLEASE / RIBONUCLEASE / DOMAIN SWAPPING / HYDROLASE / PROTEIN-PROTEIN INTERACTION
Function / homologyPancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / pancreatic ribonuclease / ribonuclease A activity / ribonuclease activity / nucleic acid binding ...Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / pancreatic ribonuclease / ribonuclease A activity / ribonuclease activity / nucleic acid binding / endonuclease activity / extracellular region / Ribonuclease pancreatic
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.1 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 12, 1998 / Release: Apr 29, 1998
RevisionDateData content typeGroupProviderType
1.0Apr 29, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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
Polyers27,4172
Non-polymers1673
Water1,65792
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4470
ΔGint (kcal/M)-49
Surface area (Å2)12630
MethodPISA
Unit cell
γ
α
β
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-MP 32

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Components

#1: Protein/peptide RIBONUCLEASE A / Pancreatic ribonuclease


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


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl / Chloride
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Formula: H2O / Water

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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 / Density percent 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
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Oct 1, 1997
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 25.5 Å2 / D resolution high: 2.1 Å / D resolution low: 4 Å / Number obs: 16601 / Observed criterion sigma I: 0 / Rsym value: 0.097 / NetI over sigmaI: 8 / Redundancy: 1.8 % / Percent possible obs: 96
Reflection shellHighest resolution: 2.1 Å / Lowest resolution: 2.18 Å / MeanI over sigI obs: 2 / Rsym value: 0.263 / Redundancy: 1.7 % / Percent possible all: 92
Reflection
*PLUS
Number 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
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTB
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 20.1 Å2
Least-squares processR factor R free: 0.256 / R factor R free error: 0.006 / R factor R work: 0.192 / R factor obs: 0.192 / Highest resolution: 2.1 Å / Lowest resolution: 1 Å / Number reflection R free: 1598 / Number reflection obs: 16471 / Percent reflection R free: 9.7 / Percent reflection obs: 96.2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 1 Å
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1902 / Nucleic acid: 0 / Ligand: 3 / Solvent: 93 / Total: 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_it0.691.50
X-RAY DIFFRACTIONx_mcangle_it1.222.00
X-RAY DIFFRACTIONx_scbond_it0.942.00
X-RAY DIFFRACTIONx_scangle_it1.552.50
Refine LS shellHighest resolution: 2.1 Å / R factor R free: 0.267 / R factor R free error: 0.019 / R factor R work: 0.253 / Lowest resolution: 2.19 Å / Number reflection R free: 197 / Number reflection R work: 1776 / Total number of bins used: 8 / Percent reflection R free: 9.16 / Percent reflection 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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