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- PDB-8iud: Crystal Structure of bacterial defense protein GajB -

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Basic information

Entry
Database: PDB / ID: 8iud
TitleCrystal Structure of bacterial defense protein GajB
ComponentsGabija protein GajB
KeywordsUNKNOWN FUNCTION / bacterial antiphage defense system / Gabija / GajB
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / defense response to virus / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOh, H. / Bae, E.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2022R1A2C1009804 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00207820 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural and functional investigation of GajB protein in Gabija anti-phage defense.
Authors: Oh, H. / Koo, J. / An, S.Y. / Hong, S.H. / Suh, J.Y. / Bae, E.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gabija protein GajB


Theoretical massNumber of molelcules
Total (without water)57,7571
Polymers57,7571
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.656, 70.261, 145.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gabija protein GajB / Putative helicase GajB


Mass: 57757.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain VD045) (bacteria)
Strain: VD045 / Gene: gajB, IIE_04983 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J8HQ06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 20 %(v/v) PEG 400, 20 %(v/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 91545 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.985 / Χ2: 0.042 / Net I/σ(I): 9.5 / Num. measured all: 689965
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.077.61.10591511.1161100
2.07-2.157.60.72491481.091100
2.15-2.257.60.55191891.081100
2.25-2.377.60.38692041.0221100
2.37-2.527.60.28492210.9921100
2.52-2.717.60.18791480.9781100
2.71-2.997.60.12891860.9111100
2.99-3.427.60.08491890.8141100
3.42-4.317.50.06691660.7071100
4.31-5070.06889430.47197

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Processing

Software
NameVersionClassification
HKL-2000v723data collection
HKL-2000v723data scaling
AutoSolphasing
PHENIX1.9_1692model building
PHENIX1.9_1692refinement
PDB_EXTRACTV4.0data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→28.468 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 3779 4.14 %
Rwork0.197 --
obs0.1986 91384 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 0 265 4138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083937
X-RAY DIFFRACTIONf_angle_d0.9535310
X-RAY DIFFRACTIONf_dihedral_angle_d12.4051487
X-RAY DIFFRACTIONf_chiral_restr0.042604
X-RAY DIFFRACTIONf_plane_restr0.004682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02430.32881170.30382892X-RAY DIFFRACTION88
2.0243-2.0510.3551510.2923263X-RAY DIFFRACTION100
2.051-2.0790.32061180.28513318X-RAY DIFFRACTION100
2.079-2.10870.31411430.25863231X-RAY DIFFRACTION100
2.1087-2.14020.33331430.25563310X-RAY DIFFRACTION100
2.1402-2.17360.291460.24433244X-RAY DIFFRACTION100
2.1736-2.20930.27851340.23883282X-RAY DIFFRACTION100
2.2093-2.24730.26881430.23323246X-RAY DIFFRACTION100
2.2473-2.28820.27051410.23553310X-RAY DIFFRACTION100
2.2882-2.33220.27471350.21753267X-RAY DIFFRACTION100
2.3322-2.37980.26891420.23193258X-RAY DIFFRACTION100
2.3798-2.43150.28811270.22213250X-RAY DIFFRACTION100
2.4315-2.4880.31381480.22043254X-RAY DIFFRACTION100
2.488-2.55020.28341360.21233280X-RAY DIFFRACTION100
2.5502-2.61910.22531400.20313275X-RAY DIFFRACTION100
2.6191-2.69610.281440.19643282X-RAY DIFFRACTION100
2.6961-2.7830.20581480.20863229X-RAY DIFFRACTION100
2.783-2.88240.2931500.22923285X-RAY DIFFRACTION100
2.8824-2.99770.26631280.21973268X-RAY DIFFRACTION100
2.9977-3.1340.23281480.21743239X-RAY DIFFRACTION100
3.134-3.2990.27711460.20723261X-RAY DIFFRACTION100
3.299-3.50530.20371380.19493294X-RAY DIFFRACTION100
3.5053-3.77540.17331430.16643246X-RAY DIFFRACTION100
3.7754-4.15430.18451400.16163265X-RAY DIFFRACTION100
4.1543-4.7530.15651460.13983256X-RAY DIFFRACTION99
4.753-5.97920.20491520.17943235X-RAY DIFFRACTION100
5.9792-28.4680.28021320.19933065X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 32.474 Å / Origin y: 60.4742 Å / Origin z: 61.3164 Å
111213212223313233
T0.3508 Å20.0154 Å20.0298 Å2-0.2592 Å2-0.0078 Å2--0.2536 Å2
L0.3969 °20.3309 °20.3247 °2-0.6149 °20.1754 °2--0.6657 °2
S-0.0452 Å °-0.0012 Å °-0.0274 Å °-0.0039 Å °0.0396 Å °-0.0319 Å °0.0171 Å °0.0013 Å °0.0063 Å °
Refinement TLS groupSelection details: all

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