PDB-4o4a: 2.75 Angstrom Crystal Structure of Putative Lipoprotein from Baci...

ID or keywords:

Entry

Database: PDB / ID: 4o4a

Title

2.75 Angstrom Crystal Structure of Putative Lipoprotein from Bacillus anthracis.

Components

Lipoprotein, putative

Keywords

LIPID BINDING PROTEIN /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID /

putative lipoprotein

Function / homology

Putative lipoprotein BA_2398-like / DI(HYDROXYETHYL)ETHER /

Lipoprotein /

Putative lipoprotein

Function and homology information

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.75 Å

Authors

Minasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 2.75 Angstrom Crystal Structure of Putative Lipoprotein from Bacillus anthracis.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 18, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4o4a.cif.gz	248.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4o4a.ent.gz	213.2 KB	Display	PDB format
PDBx/mmJSON format	4o4a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/4o4a ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o4a	HTTPS FTP

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Related structure data

Similar structure data	5whd-d 3ofk-d 5w8n-1 1tgo-d 4mrm-d 4ahc-1 4avc-d 3mwy-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: idp05469

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lipoprotein, putative

B: Lipoprotein, putative

C: Lipoprotein, putative

D: Lipoprotein, putative

hetero molecules

79.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lipoprotein, putative

D: Lipoprotein, putative

hetero molecules

B: Lipoprotein, putative

C: Lipoprotein, putative

hetero molecules

defined by author&software
79.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.556, 122.556, 107.354
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	33 - 174
2	1	B	33 - 174
1	2	A	33 - 175
2	2	C	33 - 175
1	3	A	33 - 174
2	3	D	33 - 174
1	4	B	33 - 174
2	4	C	33 - 174
1	5	B	33 - 176
2	5	D	33 - 176
1	6	C	33 - 174
2	6	D	33 - 174

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Lipoprotein, putative / / Putative lipoprotein Mass: 19671.953 Da / Num. of mol.: 4 / Fragment: Putative Lipoprotein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_2398, BAS2234, GBAA_2398 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q81QM6, UniProt: A0A6L8PAP6*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.56 Å³/Da / Density % sol: 51.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.2 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2013 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.75→30 Å / Num. all: 21759 / Num. obs: 21759 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / B_iso Wilson estimate: 70.9 Å² / R_merge(I) obs: 0.092 / R_sym value: 0.092 / Net I/σ(I): 27.5
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.543 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1055 / R_sym value: 0.543 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
SHELXS		phasing
REFMAC	5.7.0032	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.75→29.96 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.9 / SU B: 27.445 / SU ML: 0.265
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 1.047 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25278	1107	5.1 %	RANDOM
R_work	0.20918	-	-	-
all	0.21137	20596	-	-
obs	0.21137	20596	99.36 %	-

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: 65.046 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0 Å²
2-	-	0.32 Å²	-0 Å²
3-	-	-	-0.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→29.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4628	0	46	91	4765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	4770
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	4360
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.968	6449
X-RAY DIFFRACTION	r_angle_other_deg	1.128	3	10089
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.747	5	576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.498	25.102	245
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.437	15	784
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.924	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	705
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5406
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1070
X-RAY DIFFRACTION	r_mcbond_it	2.755	3.165	2313
X-RAY DIFFRACTION	r_mcbond_other	2.755	3.164	2312
X-RAY DIFFRACTION	r_mcangle_it	4.439	4.74	2886
X-RAY DIFFRACTION	r_mcangle_other	4.438	4.741	2887
X-RAY DIFFRACTION	r_scbond_it	3.884	3.728	2457
X-RAY DIFFRACTION	r_scbond_other	3.784	3.695	2441
X-RAY DIFFRACTION	r_scangle_other	5.881	5.325	3540
X-RAY DIFFRACTION	r_long_range_B_refined	8.337	25.851	5192
X-RAY DIFFRACTION	r_long_range_B_other	8.334	25.829	5182

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7017	0.17
1	2	B	7017	0.17
2	1	A	7270	0.16
2	2	C	7270	0.16
3	1	A	7154	0.16
3	2	D	7154	0.16
4	1	B	7446	0.14
4	2	C	7446	0.14
5	1	B	7470	0.13
5	2	D	7470	0.13
6	1	C	7389	0.14
6	2	D	7389	0.14

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	85	-
R_work	0.302	1417	-
obs	-	1417	96.34 %

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	3.0369	-1.1783	-0.3636	3.5403	0.0483	11.6431	0.4094	-0.1301	-0.0172	-0.3547	0.2129	0.0011	1.4805	0.2025	-0.6223	0.4351	-0.0041	-0.2005	0.0325	-0.0492	0.2214	27.2219	74.1	49.2289
2	2.7166	8.1946	0.4301	39.6659	12.3194	8.3439	-0.3195	-0.173	-0.7524	-0.6673	1.3135	-3.6205	0.333	1.6056	-0.9939	0.7178	0.2782	0.0317	0.8267	0.0408	0.668	37.8034	71.7871	47.7777
3	8.5744	0.8845	3.7096	4.5184	0.9005	2.2427	0.6856	-0.1245	-0.6018	-0.126	-0.0415	0.0055	0.2624	-0.4512	-0.644	0.1498	0.0197	-0.0804	0.3787	0.1596	0.3802	25.2938	84.7439	51.7341
4	0.219	-0.1147	0.2322	8.483	-0.4693	2.1554	0.1683	-0.0758	0.0282	0.1886	0.1041	-0.0789	1.0033	-0.1167	-0.2724	0.618	-0.0515	-0.1953	0.1144	-0.0045	0.3033	28.9693	69.2655	61.7309
5	1.5448	-0.2748	0.2945	3.6913	-0.5732	5.2056	0.1038	-0.14	0.2123	0.4622	-0.0054	0.2537	-0.4939	0.0435	-0.0983	0.2291	-0.0684	0.0285	0.052	-0.0039	0.1895	28.7602	45.324	36.4149
6	1.5098	-1.0051	-0.4591	5.1014	0.9517	4.7751	0.2133	0.0837	-0.0724	-0.2571	-0.0129	-0.0802	-0.3437	-0.1303	-0.2005	0.1878	-0.0395	-0.0749	0.0726	0.0639	0.1428	30.141	43.5481	26.7819
7	3.8685	-4.9693	-4.7404	12.8857	11.9897	21.5323	0.2211	-0.1861	-0.0605	-0.7323	-0.3077	0.051	-1.6755	-0.0328	0.0866	0.5344	-0.0202	0.0028	0.0644	0.0275	0.1801	30.0734	56.1301	20.8021
8	26.6272	6.9982	3.9837	5.0759	5.2342	6.0173	0.0587	0.728	-0.7648	0.1593	0.4418	-0.558	0.209	0.3885	-0.5005	0.5363	0.0558	-0.0371	0.1893	0.0473	0.3944	28.8343	69.218	35.7063
9	1.9862	-1.0453	-0.0826	9.9605	-2.9116	10.918	0.0024	0.0582	-0.3082	0.4534	0.651	0.0309	-0.4817	-0.5019	-0.6534	0.3557	0.2374	0.064	0.2351	0.1063	0.2897	30.003	70.2782	6.0146
10	2.6948	-1.1984	1.9751	10.6508	-1.7526	9.8077	-0.1393	-0.121	0.0368	0.5847	0.2926	-0.0844	0.0241	0.1801	-0.1533	0.3731	0.2239	0.094	0.1483	0.0778	0.1173	32.6222	67.0178	9.3368
11	2.4335	-4.9662	-0.7747	11.2746	-0.5147	4.9519	0.0374	-0.0622	0.3243	-0.1163	0.2804	-0.4391	0.1	0.0924	-0.3178	0.3157	0.1188	0.0842	0.2358	0.0725	0.2713	33.938	72.4205	-1.9216
12	5.8097	-2.5506	-1.6929	4.1636	2.4614	9.782	-0.0184	-0.3305	-0.7797	-0.0628	0.1782	0.5666	-0.1608	-0.9422	-0.1597	0.3774	0.1865	0.0442	0.2647	0.1493	0.2999	24.4301	75.4213	-5.9927
13	3.9908	0.7127	0.1288	2.4201	0.2814	4.2295	0.1882	-0.1543	0.1792	0.0577	-0.2571	0.2821	-0.0218	-0.8693	0.0689	0.0542	0.067	-0.0359	0.3949	-0.1319	0.1356	8.8122	91.5371	22.1504
14	32.1365	-22.6358	-13.4196	23.3909	13.1356	9.5526	0.5723	-0.2746	-1.0344	-0.284	-0.3113	0.6225	-0.1079	0.278	-0.261	0.305	-0.0103	-0.1013	0.2562	-0.078	0.2482	23.9795	91.0514	28.6382
15	3.4659	-1.8118	-2.2838	4.5407	3.6889	7.2728	0.1293	-0.2382	0.314	0.5211	-0.1913	-0.1597	0.4933	-0.3829	0.062	0.2413	-0.0286	-0.0562	0.2518	-0.0854	0.1136	15.3914	90.2179	34.7938
16	38.2883	-10.2514	5.5407	28.0863	-6.2918	14.9086	0.7098	0.7062	0.7048	-0.81	-1.1324	-0.0688	1.4335	1.0975	0.4226	0.5552	0.233	0.0055	0.2602	-0.0402	0.2764	27.2406	73.5832	21.4073

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 80
2	X-RAY DIFFRACTION	2	A	81 - 90
3	X-RAY DIFFRACTION	3	A	91 - 113
4	X-RAY DIFFRACTION	4	A	114 - 175
5	X-RAY DIFFRACTION	5	B	0 - 98
6	X-RAY DIFFRACTION	6	B	99 - 149
7	X-RAY DIFFRACTION	7	B	150 - 171
8	X-RAY DIFFRACTION	8	B	172 - 177
9	X-RAY DIFFRACTION	9	C	33 - 61
10	X-RAY DIFFRACTION	10	C	62 - 106
11	X-RAY DIFFRACTION	11	C	107 - 143
12	X-RAY DIFFRACTION	12	C	144 - 175
13	X-RAY DIFFRACTION	13	D	33 - 112
14	X-RAY DIFFRACTION	14	D	113 - 122
15	X-RAY DIFFRACTION	15	D	123 - 171
16	X-RAY DIFFRACTION	16	D	172 - 177

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