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- PDB-3tr8: Structure of an oligoribonuclease (orn) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tr8
TitleStructure of an oligoribonuclease (orn) from Coxiella burnetii
ComponentsOligoribonuclease
KeywordsHYDROLASE / Transcription
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA metabolic process / 3'-5'-RNA exonuclease activity / 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
ACETATE ION / : / Oligoribonuclease
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.503 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Oct 9, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Oligoribonuclease
B: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3279
Polymers42,9992
Non-polymers3277
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-60 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.656, 61.300, 58.094
Angle α, β, γ (deg.)90.000, 112.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oligoribonuclease


Mass: 21499.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_1235, orn / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83C93, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M sodium cacodylate, 0.16M magnesium acetate, 16% PEG 8000, 20% glycerol, pH 6.5, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 17, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 13417 / Num. obs: 13189 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.076 / Χ2: 1.008 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.542.50.1675090.834176.1
2.54-2.592.80.1766090.736196.2
2.59-2.643.30.1926940.781199.3
2.64-2.693.60.1496420.784199.7
2.69-2.753.70.1586750.69199.9
2.75-2.823.70.1396660.796199.9
2.82-2.893.70.1396840.825199.9
2.89-2.963.70.1176410.7611100
2.96-3.053.70.1116780.8051100
3.05-3.153.70.0996590.874199.8
3.15-3.263.70.0896660.9041100
3.26-3.393.70.086830.9181100
3.39-3.553.70.0686580.985199.8
3.55-3.733.70.076581.261100
3.73-3.973.70.0576741.1691100
3.97-4.273.60.0616721.2811100
4.27-4.73.70.0566881.428199.9
4.7-5.383.70.0576651.2041100
5.38-6.783.70.0636841.009199.9
6.78-503.50.0596841.907196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→26.025 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.7795 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 645 4.89 %RANDOM
Rwork0.2072 ---
all0.2105 13978 --
obs0.2105 13179 98.9 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.458 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso max: 67.4 Å2 / Biso mean: 25.96 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-11.828 Å20 Å22.5367 Å2
2---6.4581 Å2-0 Å2
3----5.3699 Å2
Refinement stepCycle: LAST / Resolution: 2.503→26.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 10 128 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133053
X-RAY DIFFRACTIONf_angle_d0.7254142
X-RAY DIFFRACTIONf_chiral_restr0.051467
X-RAY DIFFRACTIONf_plane_restr0.002536
X-RAY DIFFRACTIONf_dihedral_angle_d11.2091119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.503-2.69650.32221240.22782383250795
2.6965-2.96750.27051270.22125352662100
2.9675-3.39610.29961380.196325202658100
3.3961-4.27560.23871260.185225132639100
4.2756-26.02690.27811300.2212583271399

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