PDB-5ffp: Crystal structure of CdiI from Burkholderia dolosa AUO158

ID or keywords:

Entry

Database: PDB / ID: 5ffp

Title

Crystal structure of CdiI from Burkholderia dolosa AUO158

Components

Immunity 23 family protein

Keywords

ANTITOXIN / immunity protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI

Biological species

Burkholderia dolosa AU0158 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Michalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094585	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM102318	United States

Citation

Journal: To Be Published
Title: Crystal structure of CdiI from Burkholderia dolosa AUO158
Authors: Michalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Dec 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ffp.cif.gz	133.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5ffp_validation.pdf.gz	443.4 KB	Display	wwPDB validaton report
Full document	5ffp_full_validation.pdf.gz	444.8 KB	Display
Data in XML	5ffp_validation.xml.gz	12.8 KB	Display
Data in CIF	5ffp_validation.cif.gz	16.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ff/5ffp ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ffp	HTTPS FTP

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Related structure data

Similar structure data	3e0b-d 3sva-1 2d6c-d 3s67-1 1kq5-3 1g96-1 1r4c-3 1r4c-4 5eaz-1 4jnj-5 Search similar-shape structures by Omokage search (details)
Other databases	TargetTrack: MCSG-APC111477 TargetTrack: MCSG-CPX200210

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Immunity 23 family protein

B: Immunity 23 family protein

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	116.298, 116.298, 70.065
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	1 - 155
2	0	1	0	B	1 - 155

Details

AUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN AT THIS STAGE

#1: Protein	Immunity 23 family protein Mass: 19379.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia dolosa AU0158 (bacteria) / Gene: AK34_4389 / Plasmid: pMCSG58 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.57 Å³/Da / Density % sol: 65.57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M (NH4)2SO4, 0.1 sodium acetate pH 5.6, 30% PEG 4000, cryo saturated sucrose

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014 / Details: mirrors

Radiation

Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.572
1	1	K, H, -L	2	0.428

Reflection

Resolution: 2.5→30.01 Å / Num. obs: 18768 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / R_merge(I) obs: 0.13 / Net I/σ(I): 12.2

Reflection shell

Resolution: 2.5→2.54 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.587 / Mean I/σ(I) obs: 1.83 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→30.01 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.931 / SU B: 11.105 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Refinement performed against intensities.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20492	1861	9.9 %	thin resolution shells
R_work	0.19044	-	-	-
obs	0.19191	16893	99.82 %	-

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: 45.16 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	14.4 Å²	0 Å²	0 Å²
2-	-	14.4 Å²	0 Å²
3-	-	-	-28.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→30.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2420	0	15	5	2440

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	2491
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	2238
X-RAY DIFFRACTION	r_angle_refined_deg	1.432	1.956	3372
X-RAY DIFFRACTION	r_angle_other_deg	0.987	3	5160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.947	5	308
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.27	24	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.082	15	366
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.062	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	363
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2844
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	594
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	0.683	1.283	1238
X-RAY DIFFRACTION	r_mcbond_other	0.682	1.282	1237
X-RAY DIFFRACTION	r_mcangle_it	1.18	1.919	1544
X-RAY DIFFRACTION	r_mcangle_other	1.179	1.919	1545
X-RAY DIFFRACTION	r_scbond_it	1.579	1.437	1253
X-RAY DIFFRACTION	r_scbond_other	1.545	1.438	1253
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.048	2.094	1829
X-RAY DIFFRACTION	r_long_range_B_refined	3.226	10.27	2707
X-RAY DIFFRACTION	r_long_range_B_other	3.226	10.296	2708
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 8312 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.501→2.636 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.441	283	-
R_work	0.435	2392	-
obs	-	-	98.78 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3927	0.3806	-1.5603	2.028	0.2755	9.2885	0.0646	-0.0806	0.071	0.0941	0.03	-0.1583	-0.4533	0.3203	-0.0946	0.2207	0.0646	-0.0383	0.0631	-0.0535	0.2169	55.1621	3.1463	28.2626
2	14.417	-8.4488	-7.5641	6.5025	3.9677	5.1717	0.009	0.2163	0.2545	-0.095	0.0296	-0.0975	-0.0172	-0.3878	-0.0386	0.461	0.018	-0.0189	0.2004	0.0303	0.2743	52.1704	22.7809	29.2818
3	2.1286	-1.1854	-0.3931	6.028	-5.278	5.8004	0.0677	0.0634	0.374	-0.0169	0.6439	0.5726	-0.2479	-0.803	-0.7116	0.8596	0.2877	-0.0996	0.2902	-0.0546	0.5309	40.8755	20.5023	24.2668
4	4.9572	0.7942	-0.5745	8.2938	1.9535	8.2829	0.0411	-0.0386	0.0549	0.4882	-0.1095	0.4222	-0.1455	-0.7118	0.0684	0.4122	0.2124	0.0609	0.1964	0.0256	0.2165	42.128	15.4833	31.3924
5	13.0303	-1.2627	-1.4281	3.715	0.811	3.4103	0.0781	-0.5209	0.2005	-0.0942	-0.0261	-0.2082	-0.5696	0.2202	-0.0521	0.4574	0.0294	-0.0136	0.1078	-0.0081	0.1806	56.4649	14.972	35.885
6	14.093	-1.5978	-4.2108	7.9914	-5.0299	5.1417	0.0149	0.1598	0.2992	0.2123	-0.077	-0.2393	-0.1542	0.001	0.0621	0.0459	0.0295	-0.0295	0.1327	0.0656	0.0944	36.1348	42.7405	-7.6683
7	3.8424	-0.0087	0.2151	1.286	0.7052	7.47	-0.0923	-0.2129	-0.1159	-0.0288	0.0171	0.0927	0.041	-0.1567	0.0753	0.0063	0.0206	0.0112	0.1254	0.0569	0.0631	30.4285	44.6619	4.0303
8	4.8442	-3.3243	-1.0781	4.6705	0.2792	0.4659	-0.2399	-0.4139	-0.0284	0.471	0.2418	-0.512	0.2524	0.1752	-0.0019	0.5686	0.1751	-0.222	0.3388	-0.0059	0.2902	44.0113	31.3469	0.7967
9	1.8072	-0.5304	1.7737	2.1521	-2.9396	7.7423	0.2601	-0.3936	-0.792	0.1896	-0.015	0.1215	1.0118	0.2017	-0.2451	0.4741	0.1412	-0.0305	0.3415	0.1142	0.4828	40.4304	25.5019	5.3775
10	6.0684	0.0751	-1.4926	5.8836	2.078	6.8718	0.0206	0.169	-0.4501	-0.3629	0.0604	-0.3413	0.498	0.2536	-0.081	0.1622	0.1092	-0.0383	0.196	-0.0161	0.1339	39.9252	33.2977	-4.5317

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 50
2	X-RAY DIFFRACTION	2	A	51 - 68
3	X-RAY DIFFRACTION	3	A	69 - 107
4	X-RAY DIFFRACTION	4	A	108 - 135
5	X-RAY DIFFRACTION	5	A	136 - 155
6	X-RAY DIFFRACTION	6	B	1 - 11
7	X-RAY DIFFRACTION	7	B	12 - 43
8	X-RAY DIFFRACTION	8	B	44 - 76
9	X-RAY DIFFRACTION	9	B	77 - 117
10	X-RAY DIFFRACTION	10	B	118 - 155

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