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- PDB-7wik: Crystal structure of oligoribonuclease of Mycobacterium smegmatis... -

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Basic information

Entry
Database: PDB / ID: 7wik
TitleCrystal structure of oligoribonuclease of Mycobacterium smegmatis mc2 155
ComponentsOligoribonucleaseOligonucleotidase
KeywordsHYDROLASE / Oligoribonuclease / ORN / RNase H-like fold / DnaQ like exoribonuclease
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 superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / Oligoribonuclease
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBadhwar, P. / Taneja, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer.
Authors: Badhwar, P. / Khan, S.H. / Taneja, B.
History
DepositionJan 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Oligoribonuclease
D: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46536
Polymers93,0294
Non-polymers2,43532
Water11,602644
1
A: Oligoribonuclease
B: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,49315
Polymers46,5152
Non-polymers97913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-105 kcal/mol
Surface area18020 Å2
MethodPISA
2
C: Oligoribonuclease
D: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,97121
Polymers46,5152
Non-polymers1,45719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-117 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.250, 97.260, 146.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 196 / Label seq-ID: 2 - 197

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Oligoribonuclease / Oligonucleotidase


Mass: 23257.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: orn / Plasmid: pET28-His10-Smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0R1E6, EC: 3.1.13.3

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Non-polymers , 7 types, 676 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.97 % / Description: thick, long rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1M Tris-HCl, pH8.4, 0.2M Lithium sulphate, 30% v/v PEG-4000
PH range: 8-9

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.87→81.07 Å / Num. obs: 71290 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Net I/σ(I): 13.5
Reflection shellResolution: 1.874→1.906 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2 / Num. unique obs: 3483 / CC1/2: 0.803 / Rpim(I) all: 0.377 / Rrim(I) all: 0.794 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEJan 26, 2018data scaling
PDB_EXTRACT3.27data extraction
autoPROC1.1.7data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2igi

2igi


Resolution: 1.87→81.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.776 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 3553 5 %RANDOM
Rwork0.1792 ---
obs0.1813 67736 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.89 Å2 / Biso mean: 33.637 Å2 / Biso min: 16.31 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2---1.03 Å20 Å2
3----2.71 Å2
Refinement stepCycle: final / Resolution: 1.87→81.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6137 0 154 647 6938
Biso mean--47.38 43.64 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136611
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176300
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6389005
X-RAY DIFFRACTIONr_angle_other_deg1.3531.58314583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86521.078371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.068151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3021565
X-RAY DIFFRACTIONr_chiral_restr0.0720.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021379
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62660.08
12B62660.08
21A62610.07
22C62610.07
31A61850.09
32D61850.09
41B64210.07
42C64210.07
51B63120.08
52D63120.08
61C63700.09
62D63700.09
LS refinement shellResolution: 1.873→1.922 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 257 -
Rwork0.331 4886 -
all-5143 -
obs--99.38 %

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