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- PDB-1rbj: RIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE)) -

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Basic information

Entry
Database: PDB / ID: 1rbj
TitleRIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE))
Components
  • DNA (5'-D(*AP*AP*AP*A)-3')
  • PROTEIN (RIBONUCLEASE B (E.C.3.1.27.5))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA 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
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
DNA / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsKo, T.-P. / Williams, R. / McPherson, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a ribonuclease B+d(pA)4 complex.
Authors: Ko, T.P. / Williams, R. / McPherson, A.
History
DepositionMay 22, 1995Deposition site: BNL / Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*AP*AP*AP*A)-3')
A: PROTEIN (RIBONUCLEASE B (E.C.3.1.27.5))


Theoretical massNumber of molelcules
Total (without water)14,9162
Polymers14,9162
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.450, 44.450, 156.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*AP*AP*AP*A)-3')


Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (RIBONUCLEASE B (E.C.3.1.27.5))


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / Secretion: MILK / References: UniProt: P61823, EC: 3.1.27.5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Sep 11, 1984
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. obs: 3431 / % possible obs: 69.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.04
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 69.5 % / Redundancy: 2 %

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Processing

Software
NameClassification
ORESTESdata collection
TNTrefinement
ORESTESdata reduction
RefinementResolution: 2.7→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.163 3071
Displacement parametersBiso mean: 15.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 84 0 0 1035
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.020.02
X-RAY DIFFRACTIONt_angle_deg2.9823
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.020.02
X-RAY DIFFRACTIONt_it2.19
X-RAY DIFFRACTIONt_nbd0.0830.1
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.79 Å / % reflection Rfree: 34.9 % / Num. reflection obs: 160 / Rfactor obs: 0.23

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