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- PDB-7vh4: Crystal structure of oligoribonuclease of Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7vh4
TitleCrystal structure of oligoribonuclease of Escherichia coli
ComponentsOligoribonuclease
KeywordsHYDROLASE / Oligoribonuclease / ORN / RNase H-like fold / GENE REGULATION
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBadhwar, P. / Taneja, B.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
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
DepositionSep 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
D: Oligoribonuclease
C: Oligoribonuclease
B: Oligoribonuclease
A: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,19513
Polymers83,7114
Non-polymers4849
Water3,261181
1
C: Oligoribonuclease
hetero molecules

D: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1518
Polymers41,8552
Non-polymers2966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area4430 Å2
ΔGint-31 kcal/mol
Surface area15770 Å2
MethodPISA
2
B: Oligoribonuclease
A: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0445
Polymers41,8552
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.574, 100.574, 147.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-61-

TRP

21B-61-

TRP

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12D
22B
13D
23A
14C
24B
15C
25A
16B
26A

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALADA3 - 1814 - 182
21ALAALACB3 - 1814 - 182
12ALAALADA3 - 1814 - 182
22ALAALABC3 - 1814 - 182
13ALAALADA3 - 1814 - 182
23ALAALAAD3 - 1814 - 182
14ALAALACB3 - 1814 - 182
24ALAALABC3 - 1814 - 182
15ALAALACB3 - 1814 - 182
25ALAALAAD3 - 1814 - 182
16SERSERBC2 - 1813 - 182
26SERSERAD2 - 1813 - 182

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules DCBA

#1: Protein
Oligoribonuclease


Mass: 20927.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: orn / Plasmid: pET28a-His10-Smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6D2W9V9, EC: 3.1.13.3

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.25 Å3/Da / Density % sol: 45.26 % / Description: thin, flat, sheet-like
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Sodium HEPES, pH 7.5, 0.25 M Sodium acetate, 25 % v/v PEG-3350
PH range: 7-8

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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: 2.3→59.63 Å / Num. obs: 34389 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 54.922 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3274 / Rpim(I) all: 0.299 / Rrim(I) all: 0.615 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IGI

2igi


Resolution: 2.3→59.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.886 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1673 4.9 %RANDOM
Rwork0.1938 ---
obs0.1963 32650 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.25 Å2 / Biso mean: 55.092 Å2 / Biso min: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å20 Å2
2---2.77 Å20 Å2
3---5.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5705 0 30 181 5916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135964
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175555
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6448082
X-RAY DIFFRACTIONr_angle_other_deg1.2711.57812853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15621.749366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.907151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5491555
X-RAY DIFFRACTIONr_chiral_restr0.0650.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021316
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D59160.05
12C59160.05
21D58530.07
22B58530.07
31D58430.06
32A58430.06
41C58600.07
42B58600.07
51C58850.06
52A58850.06
61B59600.06
62A59600.06
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 130 -
Rwork0.298 2314 -
all-2444 -
obs--98 %

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