PDB-3imi: 2.01 Angstrom resolution crystal structure of a HIT family protei...

ID or keywords:

Entry

Database: PDB / ID: 3imi

Title

2.01 Angstrom resolution crystal structure of a HIT family protein from Bacillus anthracis str. 'Ames Ancestor'

Components

HIT family protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HIT Family Protein /

Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

catalytic activity /

metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis str. 'Ames Ancestor' (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.01 Å

Authors

Halavaty, A.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.01 Angstrom resolution crystal structure of a HIT family protein from Bacillus anthracis str. 'Ames Ancestor'
Authors: Halavaty, A.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 10, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 18, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3imi.cif.gz	130.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3imi.ent.gz	109.7 KB	Display	PDB format
PDBx/mmJSON format	3imi.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/im/3imi ftp://data.pdbj.org/pub/pdb/validation_reports/im/3imi	HTTPS FTP

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Related structure data

Similar structure data	6aif-d 5o16-2 2x6t-5 2vxy-d 2rhl-1 4tx6-2 3fkg-d 2xuc-2 4b4o-4 5mn6-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP02451

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (3) #86 - Feb 2007 Exosomes similarity (3) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: HIT family protein

B: HIT family protein

C: HIT family protein

D: HIT family protein

hetero molecules

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

1

A: HIT family protein

B: HIT family protein

hetero molecules

defined by author&software
33.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: HIT family protein

D: HIT family protein

hetero molecules

defined by author&software
33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	156.276, 46.434, 84.291
Angle α, β, γ (deg.)	90.00, 100.61, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	HIT family protein Mass: 16471.389 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria) Strain: Ames Ancestor / Gene: BAS0978, BA_1047, GBAA1047, GBAA_1047, YP_017672 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q81U41, UniProt: A0A6L7HN72*PLUS
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.28 Å³/Da / Density % sol: 46.08 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 8000, 0.2M NH4 Sulfate, 0.1M Na Cacodylate pH 6.5. Paratone-N was used for cryoprotection, 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: 0.97857 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2009 / Details: Beryllium Lenses/Diamond Laue Mono
Radiation	Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. all: 77248 / Num. obs: 77248 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 33.6 Å² / R_merge(I) obs: 0.068 / Net I/σ(I): 14.92
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.507 / Mean I/σ(I) obs: 2.67 / Num. unique all: 3868 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
CRANK		phasing
SHELXCD		phasing
SHELXE		model building
bp3		model building
SOLOMON		phasing
ARP/wARP		model building
BUCCANEER		model building
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling
bp3		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.01→30 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.957 / SU B: 6.969 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19754	1998	5 %	RANDOM
R_work	0.16091	-	-	-
all	0.16279	37836	-	-
obs	0.16279	37836	99.28 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.402 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.45 Å²	0 Å²	-0.17 Å²
2-	-	-0.39 Å²	-0 Å²
3-	-	-	-1.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4482	0	29	285	4796

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4798
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	3081
X-RAY DIFFRACTION	r_angle_refined_deg	1.472	1.928	6546
X-RAY DIFFRACTION	r_angle_other_deg	0.845	3	7618
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.877	5	606
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.28	25.801	231
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.323	15	802
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.177	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	728
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5459
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	922
X-RAY DIFFRACTION	r_mcbond_it	0.868	1.5	2958
X-RAY DIFFRACTION	r_mcbond_other	0.277	1.5	1188
X-RAY DIFFRACTION	r_mcangle_it	1.563	2	4828
X-RAY DIFFRACTION	r_scbond_it	2.616	3	1840
X-RAY DIFFRACTION	r_scangle_it	4.014	4.5	1718

LS refinement shell

Resolution: 2.01→2.06 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.226	137	-
R_work	0.193	2563	-
obs	-	2563	92.91 %

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	3.3907	-0.1931	0.6196	1.6218	0.0769	2.0684	0.0985	-0.3437	-0.2432	0.2047	0.0229	-0.1261	0.052	-0.0577	-0.1214	0.0594	-0.0033	0.0037	0.0495	0.0503	0.0916	11.3324	-6.5499	47.2025
2	3.2084	0.4679	0.5991	0.9093	-0.1526	1.348	0.0277	0.049	-0.2359	0.0612	0.0173	-0.1677	0.0975	0.2092	-0.045	0.0512	0.0276	-0.0096	0.0467	0.0174	0.1297	19.2773	-2.9686	38.4622
3	2.4487	0.7483	0.6707	1.123	0.0698	1.8793	-0.0073	0.0311	0.0359	0.0346	0.0624	0.1255	-0.0986	-0.1449	-0.055	0.0153	0.0167	0.0131	0.0229	0.0234	0.0558	7.6832	2.8674	38.8242
4	6.3416	1.6551	-0.2833	3.1794	0.0509	0.9021	-0.1313	0.1617	0.8235	-0.0525	0.1781	0.1452	-0.2282	0.0396	-0.0468	0.1593	-0.0017	-0.0158	0.0628	0.0351	0.1155	18.1078	20.1561	32.2061
5	2.6826	0.4775	0.1072	2.3099	0.4916	2.9935	-0.1538	0.5135	0.112	-0.4572	0.1746	-0.076	-0.2378	0.134	-0.0208	0.1613	-0.047	0.0175	0.1181	0.046	0.0681	20.6414	13.2402	22.3021
6	3.277	0.864	0.9539	1.627	0.1867	2.382	-0.0151	0.314	-0.1838	-0.1973	0.0748	-0.1447	-0.0033	0.0826	-0.0596	0.0321	-0.0001	0.0189	0.0308	-0.0145	0.0291	20.1746	2.9606	28.2951
7	2.9066	0.6744	0.4105	1.9048	0.1178	2.3846	-0.0044	-0.0163	0.2477	-0.0196	-0.0079	0.1518	-0.2243	-0.1054	0.0123	0.0808	0.0214	0.0057	0.0172	0.0228	0.0759	13.2963	13.588	34.4155
8	4.6407	0.1427	-2.3076	1.5002	1.1166	4.7913	0.03	0.0366	-0.1439	0.0308	-0.1193	0.146	0.1357	-0.416	0.0892	0.0737	0.0014	-0.0416	0.1301	0.0519	0.0965	-1.1268	-6.2353	42.5692
9	5.3434	0.4456	0.7964	6.2816	-1.1489	3.7962	0.039	-0.7752	-0.3458	0.7105	-0.1822	0.2891	-0.2613	-0.275	0.1432	0.4046	-0.0096	0.0348	0.399	0.1198	0.1074	0.2013	-19.2612	95.4525
10	3.2849	0.6438	0.2268	3.1791	-0.5739	3.6765	0.0173	-0.3449	-0.0525	0.4779	-0.1557	0.0315	-0.1296	0.0744	0.1383	0.1927	-0.0286	-0.0012	0.2381	0.1254	0.078	3.7371	-16.3488	84.4522
11	11.6011	13.5286	7.7036	16.9606	10.2628	6.5802	0.0487	0.1119	-1.3223	0.5768	0.6329	-1.3069	0.6222	0.9032	-0.6816	0.5136	0.1571	-0.0872	1.0325	0.2683	0.635	18.5264	-21.6395	78.7253
12	6.3374	-1.5057	-0.5097	2.6198	0.2751	7.7011	-0.0682	0.3921	-0.3061	-0.2055	-0.0222	-0.0115	0.2416	-0.3263	0.0904	0.1496	-0.0968	0.0037	0.1149	0.0588	0.2266	-1.8493	-18.4284	58.6865
13	1.7599	0.6606	-0.34	2.4211	-0.4802	3.0474	0.0006	-0.0475	0.0934	0.1684	-0.0085	0.0536	-0.3082	0.0035	0.0079	0.1177	-0.0214	-0.0191	0.105	0.0571	0.1036	1.9428	-7.074	68.2614
14	3.7899	2.0968	-0.0203	3.8712	-0.7121	3.8794	-0.0578	-0.1873	-0.3245	-0.0505	-0.0693	-0.1828	0.2391	0.1481	0.1271	0.0921	0.0011	-0.0008	0.1045	0.0972	0.0976	4.9917	-17.946	70.5281
15	6.9355	0.5143	9.5121	0.7776	0.4064	24.5562	0.2258	-0.3729	-0.5251	0.2794	-0.2535	-0.2645	0.8668	0.8116	0.0277	0.3485	0.0245	-0.0158	0.3784	0.2879	0.4338	13.4358	-27.0559	84.968
16	18.6524	-10.7207	2.7866	32.6116	-11.5825	8.6256	-0.3181	-1.0194	0.6025	1.1233	0.0339	-0.5807	-0.7843	0.7734	0.2842	0.4624	-0.1915	-0.2133	0.5751	0.0743	0.1139	14.16	-11.5153	96.6708

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 43
2	X-RAY DIFFRACTION	2	A	44 - 75
3	X-RAY DIFFRACTION	3	A	76 - 111
4	X-RAY DIFFRACTION	4	A	112 - 144
5	X-RAY DIFFRACTION	5	B	3 - 46
6	X-RAY DIFFRACTION	6	B	47 - 78
7	X-RAY DIFFRACTION	7	B	79 - 119
8	X-RAY DIFFRACTION	8	B	120 - 144
9	X-RAY DIFFRACTION	9	C	4 - 36
10	X-RAY DIFFRACTION	10	C	37 - 108
11	X-RAY DIFFRACTION	11	C	109 - 119
12	X-RAY DIFFRACTION	12	C	120 - 144
13	X-RAY DIFFRACTION	13	D	2 - 78
14	X-RAY DIFFRACTION	14	D	79 - 112
15	X-RAY DIFFRACTION	15	D	113 - 130
16	X-RAY DIFFRACTION	16	D	131 - 144

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