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Basic information

Entry
Database: PDB / ID: 1j9a
TitleOLIGORIBONUCLEASE
ComponentsOLIGORIBONUCLEASEOligonucleotidase
KeywordsHYDROLASE / RIBONUCLEASE / EXORIBONUCLEASE / OLIGORIBONUCLEASE / HAEMOPHILUS INFLUENZAE / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBonander, N. / Tordova, M. / Ladner, J.E. / Eisenstein, E. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: The Crystal Structure of Haemophilus Influenzae HI1715, an Oligoribonuclease
Authors: Bonander, N. / Tordova, M. / Ladner, J.E. / Eisenstein, E. / Gilliland, G.L.
History
DepositionMay 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OLIGORIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8833
Polymers21,6911
Non-polymers1922
Water2,504139
1
A: OLIGORIBONUCLEASE
hetero molecules

A: OLIGORIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7676
Polymers43,3822
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area4080 Å2
ΔGint-67 kcal/mol
Surface area16640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.110, 55.110, 144.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-1135-

HOH

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Components

#1: Protein OLIGORIBONUCLEASE / Oligonucleotidase / EXORIBONUCLEASE


Mass: 21691.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GENE HI1715 / Source: (natural) Haemophilus influenzae (bacteria)
References: UniProt: P45340, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 7.3
Details: Protein solution: 15 mg/mL protein in 0.01 M HEPES, 0.15 M sodium chloride, 0.005 M DTT, 0.005 M EDTA with pH 7.1-8.0. Reservoir: 2.3 M ammonium sulfate at pH 7.1-7.5. Hanging drop vapor ...Details: Protein solution: 15 mg/mL protein in 0.01 M HEPES, 0.15 M sodium chloride, 0.005 M DTT, 0.005 M EDTA with pH 7.1-8.0. Reservoir: 2.3 M ammonium sulfate at pH 7.1-7.5. Hanging drop vapor diffusion method. Drops were formed by combining 4 microliters reservoir solution with 4 microliters protein solution. Room temperature., pH 7.3

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9794, 0.9796, 0.9641, 0.9832
DetectorType: BRUKER / Detector: CCD / Date: Feb 27, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.96411
40.98321
ReflectionResolution: 2.5→20 Å / Num. obs: 14507 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SHELXphasing
RefinementResolution: 2.5→20 Å / Num. parameters: 6637 / Num. restraintsaints: 6233 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2986 715 5 %RANDOM
all0.1915 13792 --
obs0.1851 -100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1655.5
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 10 139 1656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0297
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.123
X-RAY DIFFRACTIONs_approx_iso_adps0

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