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

ID or keywords:

Entry

Database: PDB / ID: 8iud

Title

Crystal Structure of bacterial defense protein GajB

Components

Gabija protein GajB

Keywords

UNKNOWN FUNCTION / bacterial antiphage defense system / Gabija / GajB

Function / homology

Function and homology information

DNA helicase complex / recombinational repair / 3'-5' DNA helicase activity / defense response to virus / hydrolase activity / DNA binding / ATP binding / cytosol
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Oh, H. / Bae, E.

Funding support

Korea, Republic Of, 2items

Citation

Journal: 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

Deposition	Mar 24, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8iud.cif.gz	215 KB	Display	PDBx/mmCIF format
PDB format	pdb8iud.ent.gz	172.5 KB	Display	PDB format
PDBx/mmJSON format	8iud.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8iud_validation.pdf.gz	424.4 KB	Display	wwPDB validaton report
Full document	8iud_full_validation.pdf.gz	427.2 KB	Display
Data in XML	8iud_validation.xml.gz	20.1 KB	Display
Data in CIF	8iud_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iu/8iud ftp://data.pdbj.org/pub/pdb/validation_reports/iu/8iud	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#172 - Apr 2014 RecA and Rad51 similarity (5) #168 - Dec 2013 DNA Helicase similarity (3)

Deposited unit

A: Gabija protein GajB

57.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

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 number	19
Space group name H-M	P2₁2₁2₁

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 61 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 3, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 91545 / % possible obs: 99.7 % / Redundancy: 7.5 % / R_merge(I) obs: 0.985 / Χ²: 0.042 / Net I/σ(I): 9.5 / Num. measured all: 689965

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2-2.07	7.6	1.105	9151	1.116	1	100
2.07-2.15	7.6	0.724	9148	1.09	1	100
2.15-2.25	7.6	0.551	9189	1.08	1	100
2.25-2.37	7.6	0.386	9204	1.022	1	100
2.37-2.52	7.6	0.284	9221	0.992	1	100
2.52-2.71	7.6	0.187	9148	0.978	1	100
2.71-2.99	7.6	0.128	9186	0.911	1	100
2.99-3.42	7.6	0.084	9189	0.814	1	100
3.42-4.31	7.5	0.066	9166	0.707	1	100
4.31-50	7	0.068	8943	0.47	1	97

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Processing

Software

Name	Version	Classification
HKL-2000	v723	data collection
HKL-2000	v723	data scaling
AutoSol		phasing
PHENIX	1.9_1692	model building
PHENIX	1.9_1692	refinement
PDB_EXTRACT	V4.0	data extraction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2335	3779	4.14 %
R_work	0.197	-	-
obs	0.1986	91384	99.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→28.468 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3873	0	0	265	4138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3937
X-RAY DIFFRACTION	f_angle_d	0.953	5310
X-RAY DIFFRACTION	f_dihedral_angle_d	12.405	1487
X-RAY DIFFRACTION	f_chiral_restr	0.042	604
X-RAY DIFFRACTION	f_plane_restr	0.004	682

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.0243	0.3288	117	0.3038	2892	X-RAY DIFFRACTION	88
2.0243-2.051	0.355	151	0.292	3263	X-RAY DIFFRACTION	100
2.051-2.079	0.3206	118	0.2851	3318	X-RAY DIFFRACTION	100
2.079-2.1087	0.3141	143	0.2586	3231	X-RAY DIFFRACTION	100
2.1087-2.1402	0.3333	143	0.2556	3310	X-RAY DIFFRACTION	100
2.1402-2.1736	0.29	146	0.2443	3244	X-RAY DIFFRACTION	100
2.1736-2.2093	0.2785	134	0.2388	3282	X-RAY DIFFRACTION	100
2.2093-2.2473	0.2688	143	0.2332	3246	X-RAY DIFFRACTION	100
2.2473-2.2882	0.2705	141	0.2355	3310	X-RAY DIFFRACTION	100
2.2882-2.3322	0.2747	135	0.2175	3267	X-RAY DIFFRACTION	100
2.3322-2.3798	0.2689	142	0.2319	3258	X-RAY DIFFRACTION	100
2.3798-2.4315	0.2881	127	0.2221	3250	X-RAY DIFFRACTION	100
2.4315-2.488	0.3138	148	0.2204	3254	X-RAY DIFFRACTION	100
2.488-2.5502	0.2834	136	0.2123	3280	X-RAY DIFFRACTION	100
2.5502-2.6191	0.2253	140	0.2031	3275	X-RAY DIFFRACTION	100
2.6191-2.6961	0.28	144	0.1964	3282	X-RAY DIFFRACTION	100
2.6961-2.783	0.2058	148	0.2086	3229	X-RAY DIFFRACTION	100
2.783-2.8824	0.293	150	0.2292	3285	X-RAY DIFFRACTION	100
2.8824-2.9977	0.2663	128	0.2197	3268	X-RAY DIFFRACTION	100
2.9977-3.134	0.2328	148	0.2174	3239	X-RAY DIFFRACTION	100
3.134-3.299	0.2771	146	0.2072	3261	X-RAY DIFFRACTION	100
3.299-3.5053	0.2037	138	0.1949	3294	X-RAY DIFFRACTION	100
3.5053-3.7754	0.1733	143	0.1664	3246	X-RAY DIFFRACTION	100
3.7754-4.1543	0.1845	140	0.1616	3265	X-RAY DIFFRACTION	100
4.1543-4.753	0.1565	146	0.1398	3256	X-RAY DIFFRACTION	99
4.753-5.9792	0.2049	152	0.1794	3235	X-RAY DIFFRACTION	100
5.9792-28.468	0.2802	132	0.1993	3065	X-RAY DIFFRACTION	94

Refinement TLS params.

Method: refined / Origin x: 32.474 Å / Origin y: 60.4742 Å / Origin z: 61.3164 Å

	11	12	13	21	22	23	31	32	33
T	0.3508 Å²	0.0154 Å²	0.0298 Å²	-	0.2592 Å²	-0.0078 Å²	-	-	0.2536 Å²
L	0.3969 °²	0.3309 °²	0.3247 °²	-	0.6149 °²	0.1754 °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 group

Selection details: all

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