PDB-9atx: AcpB protein from Bacillus anthracis, N-terminal part

ID or keywords:

Entry

Database: PDB / ID: 9atx

Title

AcpB protein from Bacillus anthracis, N-terminal part

Components

Capsule synthesis positive regulator AcpB

Keywords

TRANSCRIPTION / AcpB / transcription regulator / virulence / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID

Function / homology

Function and homology information

regulation of DNA-templated transcription
Similarity search - Function

Biological species

Bacillus anthracis str. Ames (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.11 Å

Authors

Osipiuk, J. / Koehler, T.M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00035	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01 AI033537	United States

Citation

Journal: To Be Published
Title: AcpB protein from Bacillus anthracis, N-terminal part
Authors: Osipiuk, J. / Koehler, T.M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

History

Deposition	Feb 27, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9atx.cif.gz	128.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9atx.ent.gz	98.7 KB	Display	PDB format
PDBx/mmJSON format	9atx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/at/9atx ftp://data.pdbj.org/pub/pdb/validation_reports/at/9atx	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
Other databases	TargetTrack: IDP01167

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Capsule synthesis positive regulator AcpB

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.546, 63.520, 119.426
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Capsule synthesis positive regulator AcpB Mass: 32998.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Three N-terminal residues, SNA, are cloning artifacts Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria) Gene: acpB, pXO2-53, BXB0060, GBAA_pXO2_0060 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RMX9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.02 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 4.3% PEG-3000, 25% PEG-1000, 0.05 M Bicine pH 8.8

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.11→43.54 Å / Num. obs: 20624 / % possible obs: 97.5 % / Redundancy: 5.6 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.028 / R_rim(I) all: 0.07 / Χ²: 1.136 / Net I/av σ(I): 26 / Net I/σ(I): 7.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.11-2.15	2	0.721	1.08	744	0.503	0.818	0.554	0.915	1.057	74
2.15-2.19	2.4	0.678		903	0.538	0.837	0.479	0.836	1.051	85.3
2.19-2.23	3	0.622		957	0.638	0.883	0.396	0.742	0.987	93.1
2.23-2.27	3.8	0.576		1012	0.72	0.915	0.33	0.668	1.037	97.6
2.27-2.32	4.5	0.479		1039	0.834	0.954	0.247	0.541	1.035	99.5
2.32-2.38	5.3	0.434		1038	0.867	0.964	0.206	0.482	1.044	99.7
2.38-2.44	5.4	0.375		1032	0.905	0.975	0.175	0.415	1.077	99.9
2.44-2.5	6	0.324		1031	0.933	0.983	0.143	0.355	1.039	99.9
2.5-2.58	6.6	0.28		1055	0.957	0.989	0.117	0.304	1.04	100
2.58-2.66	6.7	0.236		1050	0.968	0.992	0.099	0.256	1.077	99.7
2.66-2.75	6.6	0.188		1044	0.983	0.996	0.079	0.205	1.089	100
2.75-2.86	6.5	0.15		1055	0.987	0.997	0.064	0.164	1.059	100
2.86-2.99	5.9	0.114		1035	0.991	0.998	0.051	0.125	1.077	99.6
2.99-3.15	6.6	0.094		1074	0.995	0.999	0.039	0.102	1.117	100
3.15-3.35	6.7	0.079		1059	0.995	0.999	0.033	0.086	1.182	100
3.35-3.61	6.6	0.058		1058	0.998	0.999	0.025	0.063	1.208	99.9
3.61-3.97	6	0.049		1075	0.998	1	0.022	0.053	1.309	100
3.97-4.54	6.7	0.043		1081	0.998	1	0.018	0.046	1.303	100
4.54-5.72	6.2	0.04		1102	0.998	1	0.017	0.044	1.227	99.7
5.72-43.54	5.8	0.035		1180	0.999	1	0.016	0.038	1.333	99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data scaling
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.11→43.54 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.945 / SU B: 12.568 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24552	1024	5 %	RANDOM
R_work	0.20104	-	-	-
obs	0.20338	19550	97.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 53.577 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.21 Å²	0 Å²	0 Å²
2-	-	0.37 Å²	-0 Å²
3-	-	-	-1.57 Å²

Refinement step

Cycle: 1 / Resolution: 2.11→43.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2268	0	0	57	2325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2336
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2394
X-RAY DIFFRACTION	r_angle_refined_deg	1.675	1.876	3138
X-RAY DIFFRACTION	r_angle_other_deg	0.544	1.791	5523
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.492	5	272
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.457	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.298	10	493
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	356
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2593
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	537
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.22	4.299	1076
X-RAY DIFFRACTION	r_mcbond_other	4.22	4.3	1076
X-RAY DIFFRACTION	r_mcangle_it	5.958	7.702	1343
X-RAY DIFFRACTION	r_mcangle_other	5.956	7.705	1344
X-RAY DIFFRACTION	r_scbond_it	5.027	5.011	1260
X-RAY DIFFRACTION	r_scbond_other	5.015	5.008	1259
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.948	8.918	1793
X-RAY DIFFRACTION	r_long_range_B_refined	9.969	43.22	2681
X-RAY DIFFRACTION	r_long_range_B_other	9.969	43.17	2669
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.11→2.162 Å

	R_factor	Num. reflection	% reflection
R_free	0.336	57	-
R_work	0.324	1088	-
obs	-	-	75.53 %

Refinement TLS params.

Method: refined / Origin x: 30.1551 Å / Origin y: 32.6906 Å / Origin z: 11.6715 Å

	11	12	13	21	22	23	31	32	33
T	0.05 Å²	-0.0304 Å²	-0.0363 Å²	-	0.0189 Å²	0.0174 Å²	-	-	0.1036 Å²
L	0.4556 °²	0.1768 °²	-0.1848 °²	-	0.5684 °²	-0.1965 °²	-	-	0.3743 °²
S	0.1126 Å °	-0.0679 Å °	-0.0208 Å °	-0.0093 Å °	0.0182 Å °	-0.0808 Å °	0.0339 Å °	-0.0192 Å °	-0.1308 Å °

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