PDB-2vzy: Crystal structure of Rv0802c from Mycobacterium tuberculosis in a...

ID or keywords:

Entry

Database: PDB / ID: 2vzy

Title

Crystal structure of Rv0802c from Mycobacterium tuberculosis in an unliganded form.

Components

RV0802C

Keywords

TRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE /

MYCOBACTERIUM TUBERCULOSIS / RV0802C / SUCCINYLTRANSFERASE

Function / homology

Function and homology information

N-terminal peptidyl-serine acetylation /

Transferases; Transferring sulfur-containing groups; CoA-transferases /

Transferases; Transferring sulfur-containing groups; Sulfurtransferases / peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / succinyl-CoA metabolic process / peptide-lysine-N-acetyltransferase activity /

cytoplasm
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2 Å

Authors

Vetting, M.W. / Errey, J.C. / Blanchard, J.S.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Rv0802C from Mycobacterium Tuberculosis: The First Structure of a Succinyltransferase with the Gnat Fold.
Authors: Vetting, M.W. / Errey, J.C. / Blanchard, J.S.

History

Deposition	Aug 7, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2vzy.cif.gz	174.1 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2vzy.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/vz/2vzy ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzy	HTTPS FTP

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Related structure data

Related structure data	2vzzC C: citing same article (ref.)
Similar structure data	2vzz-d 5wb3-1 5dbs-2 5wfz-2 5w9g-2 5vrj-2 5vp8-1 6fc4-d 4e5e-d 5vpt-2 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
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#35 - Nov 2002
Ferritin and Transferrin
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (3)
#97 - Jan 2008
Circadian Clock Proteins
similarity (3)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: RV0802C

B: RV0802C

C: RV0802C

D: RV0802C

hetero molecules

102 kDa, 4 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)	70.705, 111.458, 135.238
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	RV0802C Mass: 25015.283 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET23B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3(ROSETTA2) / References: UniProt: O06632, UniProt: P9WQG7*PLUS

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Non-polymers , 6 types, 597 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#5: Chemical	ChemComp-FLC / CITRATE ANION / Citric acid Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#6: Chemical	ChemComp-SM / SAMARIUM (III) ION / Samarium Mass: 150.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sm
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.79 Å³/Da / Density % sol: 55.56 % Description: DATASET INCLUDES HEAVY ATOM USED TO DETERMINE STRUCTURE BY SAD
Crystal grow	pH: 5.25 Details: PROTEIN AT 7MG/ML IN 10 MM TEA PH 7.8, 100 MM AMMONIUM SULFATE, 3% GLYCEROL, 1 MM EDTA, 2 MM DTT CRYSTALLIZED IN 150 MM NACITRATE PH 5.25

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
Detector	Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 20, 2003 / Details: OSMIC BLUE CONFOCAL
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→86 Å / Num. obs: 69624 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_merge(I) obs: 0.05 / Net I/σ(I): 22.3
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.18 / Mean I/σ(I) obs: 4.8 / % possible all: 79.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	RESOLVE	phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2→86.07 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 5.752 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.205	3524	5.1 %	RANDOM
R_work	0.164	-	-	-
obs	0.166	66073	95.5 %	-

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: 19.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	0 Å²	0 Å²
2-	-	1.17 Å²	0 Å²
3-	-	-	-0.59 Å²

Refinement step

Cycle: LAST / Resolution: 2→86.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6149	0	93	581	6823

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	6363
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.546	1.958	8614
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.571	5	755
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.824	22.216	334
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.061	15	1020
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.233	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	925
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4948
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	2671
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	4261
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	578
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	0.219	0.2	73
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.145	0.2	30
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	0.841	1.5	3922
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.379	2	6089
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.414	3	2793
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.798	4.5	2525
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.249	171
R_work	0.182	3925

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	0.9019	0.1019	-0.1951	3.0126	1.3263	1.8293	0.0668	-0.0756	0.2013	-0.1075	0.0808	-0.1467	-0.1506	0.1816	-0.1476	-0.0428	-0.0171	-0.0045	0.0338	-0.0513	0.0741	10.398	42.879	13.643
2	1.6232	-0.2932	0.453	1.3039	0.2952	1.3527	0.06	0.0065	0.1206	0.0249	0.0221	-0.0912	-0.0734	0.0327	-0.0821	-0.0309	-0.0009	-0.0052	0.0225	-0.0018	0.0415	-0.074	37.663	8.417
3	2.5042	-1.6899	0.4246	6.4011	-1.19	1.5316	0.1544	0.0961	0.1411	-0.149	-0.0265	-0.0869	0.074	0.0649	-0.1279	-0.0172	-0.013	0.0037	0.0617	-0.0053	0.045	-9.987	39.353	-1.3
4	2.3327	-0.8311	-0.5953	0.9549	0.5414	4.12	0.0509	-0.0697	-0.0961	0.0962	-0.062	0.0732	0.2933	-0.2195	0.0111	0.0081	-0.0207	-0.0172	0.0214	-0.0067	0.0631	0.187	25.727	13.473
5	1.365	0.2382	0.3375	1.5166	1.0778	1.6031	0.1091	-0.0118	-0.0192	0.0887	0.0792	-0.0234	0.1419	0.1244	-0.1883	-0.0152	-0.0125	0.0138	0.0115	-0.0709	0.0809	11.987	52.721	27.843
6	3.2473	-0.8562	-0.3283	2.1098	0.6479	2.2608	0.0279	0.0297	0.1111	-0.0821	0.132	-0.2569	0.0998	0.1787	-0.16	-0.0249	-0.0065	0.0081	0.0289	-0.0447	0.0786	11.272	63.44	34.736
7	4.1882	0.1285	-0.6235	1.6306	0.3776	1.1957	0.0979	-0.2968	0.1617	0.1053	0.096	-0.165	0.0225	0.2336	-0.1939	-0.0147	0.0338	-0.0253	0.0618	-0.0684	0.0653	4.575	67.571	44.999
8	7.1616	-1.9933	5.8791	2.7227	-0.3817	11.3451	0.0725	0.6468	0.5993	-0.4328	-0.0084	-0.2831	-0.2655	0.8562	-0.064	-0.0877	-0.0742	0.1122	-0.0062	0.0003	0.1285	18.723	68.101	25.441
9	2.1236	0.9035	0.9268	1.5547	2.1219	4.1885	0.109	-0.2054	0.1262	0.192	-0.289	0.165	0.1978	-0.3207	0.18	-0.0266	-0.0113	0.0178	0.0686	-0.1093	-0.0255	-35.059	58.459	16.387
10	8.3817	0.018	-2.938	2.1584	0.5281	2.8498	0.1445	-0.3361	0.2899	0.0663	-0.1544	-0.1169	-0.1809	-0.0321	0.0099	0.0163	-0.0378	-0.0251	0.0421	-0.0488	0.0193	-27.789	56.098	7.279
11	1.1532	-0.4435	0.0819	1.2929	0.3694	1.4545	0.0731	-0.0848	-0.0069	-0.0257	-0.2001	0.0739	-0.0557	-0.1367	0.127	-0.0616	-0.0104	0.0057	0.0749	-0.0436	0.0291	-30.323	44.339	3.331
12	4.2688	1.9602	1.6199	8.5648	5.2489	7.1458	-0.054	0.2074	0.5501	-0.6036	-0.3526	0.2263	-0.7142	-0.4093	0.4067	0.0116	0.0727	-0.0341	0.0384	0.044	-0.0411	-33.676	61.815	-0.873
13	1.6144	-0.8749	0.2862	2.2417	0.9381	3.759	0.0467	0.1632	0.0496	-0.2444	-0.0656	0.112	-0.0925	-0.1054	0.0189	-0.0197	0.0126	-0.0515	0.0774	-0.0936	0.0417	-30.523	68.617	28.481
14	4.6889	-1.9688	1.5914	4.6476	-1.4204	3.604	0.1089	0.0322	-0.1402	-0.1667	-0.1324	0.2138	0.124	-0.1897	0.0235	0.0295	-0.0088	-0.0096	0.05	-0.0639	0.0695	-23.537	66.108	37.316
15	1.6943	-0.0679	-0.2154	1.5462	-0.4003	1.6629	0.0029	-0.0334	0.1051	-0.1026	-0.0629	0.0306	-0.0491	-0.0761	0.06	0.0057	0.0309	-0.0242	-0.003	-0.0433	0.0306	-17.471	76.273	41.445
16	4.1133	2.3068	2.1192	10.4001	4.9018	7.4041	0.0607	-0.3069	-0.2916	0.3289	-0.2721	0.3889	0.4883	-0.6316	0.2114	-0.0692	-0.0417	0.0458	0.0609	0.009	-0.024	-31.077	63.319	45.407

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 65
2	X-RAY DIFFRACTION	2	A	66 - 157
3	X-RAY DIFFRACTION	3	A	158 - 188
4	X-RAY DIFFRACTION	4	A	189 - 212
5	X-RAY DIFFRACTION	5	B	2 - 75
6	X-RAY DIFFRACTION	6	B	76 - 146
7	X-RAY DIFFRACTION	7	B	147 - 194
8	X-RAY DIFFRACTION	8	B	195 - 211
9	X-RAY DIFFRACTION	9	C	2 - 73
10	X-RAY DIFFRACTION	10	C	74 - 108
11	X-RAY DIFFRACTION	11	C	109 - 192
12	X-RAY DIFFRACTION	12	C	193 - 211
13	X-RAY DIFFRACTION	13	D	2 - 74
14	X-RAY DIFFRACTION	14	D	75 - 107
15	X-RAY DIFFRACTION	15	D	108 - 193
16	X-RAY DIFFRACTION	16	D	194 - 211

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