PDB-7bra: Bacillus subtilis IRG1

ID or keywords:

Entry

Database: PDB / ID: 7bra

Title

Bacillus subtilis IRG1

Components

Bacillus subtilis IRG1

Keywords

STRUCTURAL PROTEIN / IRG1 / cis-Aconitate decarboxylase / Immune-responsive gene 1 protein

Function / homology

Function and homology information

lyase activity
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.785 Å

Authors

Park, H.H. / Chun, H.L.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Sci Rep / Year: 2020
Title: Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis.
Authors: Chun, H.L. / Lee, S.Y. / Lee, S.H. / Lee, C.S. / Park, H.H.

History

Deposition	Mar 27, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bra.cif.gz	200.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7bra.ent.gz	156.8 KB	Display	PDB format
PDBx/mmJSON format	7bra.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7bra_validation.pdf.gz	467.2 KB	Display	wwPDB validaton report
Full document	7bra_full_validation.pdf.gz	474.9 KB	Display
Data in XML	7bra_validation.xml.gz	41.7 KB	Display
Data in CIF	7bra_validation.cif.gz	63.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/7bra ftp://data.pdbj.org/pub/pdb/validation_reports/br/7bra	HTTPS FTP

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Related structure data

Related structure data	2hp0S S: Starting model for refinement
Similar structure data	7e9d-d 6qii-d 1fpm-2 4h0y-d 1eg7-2 3l2d-3 4fl9-d 6ruz-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Bacillus subtilis IRG1

B: Bacillus subtilis IRG1

hetero molecules

96.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	59.213, 110.870, 167.652
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bacillus subtilis IRG1 Mass: 47851.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54956*PLUS
#2: Chemical	ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₉NO₃S / Comment: pH buffer*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.82 Å³/Da / Density % sol: 56.4 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M CAPS pH 9.8 1.5M Ammonium sulfate 0.2M Lithium sulfate

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Data collection

Diffraction	Mean temperature: 125 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 18, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.78→39.39 Å / Num. obs: 105057 / % possible obs: 99.8 % / Redundancy: 12.3 % / R_sym value: 0.085 / Net I/σ(I): 30.47
Reflection shell	Resolution: 1.78→1.82 Å / Num. unique obs: 6857 / R_sym value: 1.13

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2HP0

2hp0

Resolution: 1.785→39.387 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.956 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2009	5250	5.002 %
R_work	0.1746	-	-
all	0.176	-	-
obs	-	104967	99.382 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 24.257 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.433 Å²	0 Å²	0 Å²
2-	-	-0.286 Å²	0 Å²
3-	-	-	-1.147 Å²

Refinement step

Cycle: LAST / Resolution: 1.785→39.387 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6734	0	38	886	7658

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	6910
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	6476
X-RAY DIFFRACTION	r_angle_refined_deg	1.819	1.641	9364
X-RAY DIFFRACTION	r_angle_other_deg	2.32	1.58	14998
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.64	5	888
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.469	21.886	350
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.958	15	1118
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.441	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.261	0.2	914
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7850
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1438
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	1636
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	6338
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3523
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	3216
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.262	0.2	602
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.221	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.124	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.334	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	2.165	2.367	3558
X-RAY DIFFRACTION	r_mcbond_other	2.166	2.367	3557
X-RAY DIFFRACTION	r_mcangle_it	2.709	3.536	4444
X-RAY DIFFRACTION	r_mcangle_other	2.709	3.537	4445
X-RAY DIFFRACTION	r_scbond_it	3.285	2.698	3352
X-RAY DIFFRACTION	r_scbond_other	3.285	2.696	3345
X-RAY DIFFRACTION	r_scangle_it	4.554	3.913	4920
X-RAY DIFFRACTION	r_scangle_other	4.555	3.908	4909
X-RAY DIFFRACTION	r_lrange_it	5.055	30.461	8200
X-RAY DIFFRACTION	r_lrange_other	4.975	29.611	7936

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 (%)
1.785-1.831	0.296	352	0.25	6907	X-RAY DIFFRACTION	94.236
1.831-1.882	0.256	394	0.233	7144	X-RAY DIFFRACTION	99.4984
1.882-1.936	0.272	384	0.221	6859	X-RAY DIFFRACTION	99.328
1.936-1.996	0.233	345	0.204	6726	X-RAY DIFFRACTION	99.1447
1.996-2.061	0.228	347	0.195	6542	X-RAY DIFFRACTION	99.884
2.061-2.133	0.213	347	0.18	6322	X-RAY DIFFRACTION	99.9251
2.133-2.214	0.198	339	0.175	6092	X-RAY DIFFRACTION	99.9068
2.214-2.304	0.196	290	0.169	5941	X-RAY DIFFRACTION	99.9679
2.304-2.407	0.198	311	0.17	5648	X-RAY DIFFRACTION	99.9497
2.407-2.524	0.204	268	0.169	5463	X-RAY DIFFRACTION	99.9477
2.524-2.66	0.204	277	0.165	5176	X-RAY DIFFRACTION	99.9633
2.66-2.822	0.213	244	0.168	4931	X-RAY DIFFRACTION	100
2.822-3.016	0.184	230	0.164	4635	X-RAY DIFFRACTION	99.9794
3.016-3.258	0.19	236	0.17	4299	X-RAY DIFFRACTION	99.978
3.258-3.568	0.201	228	0.168	3954	X-RAY DIFFRACTION	99.8806
3.568-3.988	0.184	175	0.156	3643	X-RAY DIFFRACTION	99.9215
3.988-4.604	0.158	172	0.145	3225	X-RAY DIFFRACTION	100
4.604-5.635	0.226	132	0.183	2758	X-RAY DIFFRACTION	99.9654
5.635-7.955	0.173	112	0.203	2184	X-RAY DIFFRACTION	100
7.955-30	0.173	67	0.169	1268	X-RAY DIFFRACTION	98.4513

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