PDB-2vzz: Crystal structure of Rv0802c from Mycobacterium tuberculosis in C...

ID or keywords:

Entry

Database: PDB / ID: 2vzz

Title

Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA

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 /

MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vzz.cif.gz	191 KB	Display	PDBx/mmCIF format
PDB format	pdb2vzz.ent.gz	154.9 KB	Display	PDB format
PDBx/mmJSON format	2vzz.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/2vzz ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzz	HTTPS FTP

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Related structure data

Related structure data	2vzySC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vzy-d 6fc4-d 5wb3-1 5w9g-2 5dbs-2 5ohu-d 5wfz-2 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: RV0802C

B: RV0802C

C: RV0802C

D: RV0802C

hetero molecules

104 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)	113.165, 135.172, 164.077
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#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
#2: Chemical	ChemComp-SCA / SUCCINYL-COENZYME A / Succinyl-CoA Mass: 867.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₅H₄₀N₇O₁₉P₃S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 413 / 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: 3.03 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	pH: 7 Details: PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT ...Details: PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT SOLUTION PLUS 20 MM SUCCOA AND 20% GLYCEROL

Crystal

Density Matthews: 3.03 Å³/Da / Density % sol: 54 % / Description: NONE

Crystal grow

pH: 7
Details: PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT ...

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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: Mar 16, 2004 / 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: 2.3→104 Å / Num. obs: 53759 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3 % / R_merge(I) obs: 0.2 / Mean I/σ(I) obs: 4.8 / % possible all: 92.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VZY

2vzy

Resolution: 2.3→104.26 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.915 / SU B: 10.138 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	2730	5.1 %	RANDOM
R_work	0.169	-	-	-
obs	0.172	51029	95.8 %	-

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: 19.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.33 Å²	0 Å²	0 Å²
2-	-	1.26 Å²	0 Å²
3-	-	-	-1.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→104.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6763	0	220	413	7396

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	7179
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.979	9778
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.914	5	836
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.199	21.957	368
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.568	15	1112
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.542	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1044
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5596
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	3033
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	4804
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	483
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	0.188	0.2	38
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.155	0.2	8
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	0.779	1.5	4291
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.321	2	6734
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.247	3	3305
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.623	4.5	3044
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: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.288	209	-
R_work	0.198	3573	-
obs	-	-	91.62 %

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	0.6265	-0.2685	-0.1391	0.26	0.061	0.5565	-0.0131	0.0423	-0.0078	0.0355	0.04	0.0158	0.0389	0.0568	-0.0268	0.0075	0.0019	-0.001	0.0412	-0.0027	0.0201	32.3265	37.8622	-0.7157
2	0.5772	-0.402	0.0034	0.2842	0.0277	0.2131	-0.0241	0.0286	-0.0546	0.0328	0.0646	-0.0173	-0.0898	-0.0019	-0.0404	0.0548	-0.0114	-0.0032	0.0083	0.0065	0.0261	26.7015	49.2006	1.3593
3	0.5666	0.4135	0.9479	1.2738	0.6766	2.228	-0.0306	0.0145	0.0572	0.0445	-0.0184	0.0892	-0.1909	-0.1136	0.049	0.0517	0.0367	0.0156	-0.0242	0.0045	0.0255	17.4832	54.2593	-2.2192
4	6.3765	-1.541	-3.2727	1.4759	1.2718	3.8868	0.019	-0.3395	0.1567	0.059	0.1083	-0.2101	-0.3366	0.4278	-0.1273	0.0311	-0.0781	-0.0255	-0.0593	-0.0362	0.0119	39.1085	54.6771	5.1446
5	0.5542	-0.0134	0.0157	0.5403	0.3308	1.5763	0.08	0.1212	-0.0816	0.0271	-0.0008	-0.1077	-0.3036	-0.1088	-0.0792	0.0823	0.0648	0.004	-0.0145	-0.0004	-0.0015	20.8659	56.5659	-37.5864
6	0.7151	0.1791	-0.6628	2.6931	-2.0685	4.0165	0.1469	0.0908	-0.0275	0.0733	-0.1954	-0.0916	-0.1651	-0.105	0.0485	0.0422	0.0729	-0.0215	0.0157	-0.038	-0.0037	13.058	52.6344	-30.474
7	0.994	0.3988	-0.7642	1.167	-0.6838	2.2206	0.0888	0.0997	-0.0196	-0.0495	-0.0821	-0.0789	-0.3052	-0.3676	-0.0068	0.0993	0.1379	-0.0023	0.0179	-0.0215	-0.0072	9.9292	60.3867	-29.8126
8	1.2974	0.0479	-0.0968	0.3689	-0.0313	1.7233	0.1394	-0.0756	0.0287	0.0338	-0.1626	0.0404	-0.3705	-0.366	0.0232	0.0525	0.0989	0.0002	-0.009	0.0023	-0.0259	10.3553	59.3817	-22.7146
9	0.0376	-0.1067	0.0858	0.4718	0.116	0.9565	-0.0192	-0.1325	-0.0422	0.1104	0.0071	-0.0156	0.1419	0.2021	0.0121	-0.0027	0.0478	-0.0085	0.1084	-0.0062	0.0087	49.3742	25.1508	-6.3017
10	3.5182	-1.5954	-4.0112	3.5364	0.3742	6.957	0.3185	0.1493	0.3157	-0.2808	-0.218	-0.2373	-0.4001	1.0244	-0.1006	-0.1191	-0.0617	0.003	0.3561	0.0013	-0.0412	58.9259	39.8459	-19.4498
11	0.4739	0.0376	-0.2553	0.3582	0.1711	1.1706	-0.0077	-0.0015	-0.0341	0.0326	0.0176	0.031	0.1293	0.1671	-0.0099	-0.0146	0.0441	-0.0082	0.0874	-0.0151	-0.0026	50.7056	24.5578	-18.8713
12	0.4746	0.0399	-0.2354	1.4398	-0.3997	1.9347	-0.0875	0.039	-0.0455	-0.0792	0.0407	-0.0383	0.3844	0.2258	0.0468	-0.0343	0.0767	-0.0374	0.0327	-0.0483	0.0079	50.6207	18.9035	-25.2284
13	0.3127	-0.0775	0.0781	0.6029	0.1625	0.9672	0.0273	0.0024	-0.0074	0.0007	0.0084	0.0185	-0.0252	-0.0915	-0.0357	0.0145	0.0209	-0.0069	0.0175	-0.0216	0.0248	26.6807	37.932	-47.2564
14	0.675	-0.1162	0.3125	0.6615	-0.1361	0.7519	0.0337	0.0379	0.0284	0.0002	-0.0203	-0.0103	0.0315	0.0791	-0.0134	0.0151	0.0214	0.0016	0.0355	-0.0323	0.0147	38.5239	34.2702	-50.153
15	1.3093	0.0802	-0.4095	1.3899	-0.4982	1.3274	0.0414	-0.0151	-0.0594	-0.0432	-0.083	-0.0955	0.2145	0.1275	0.0416	-0.0011	0.0291	-0.0183	0.0394	-0.0448	-0.0086	43.4593	23.4441	-43.2917
16	1.9874	-1.4678	-0.8425	3.7799	0.6382	2.8172	0.1001	0.1505	0.2703	-0.221	-0.002	-0.2576	-0.1987	0.3846	-0.0982	-0.0492	-0.0932	0.0326	0.0506	-0.0029	0.0008	45.9737	42.7435	-55.6117

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 88
2	X-RAY DIFFRACTION	2	A	89 - 156
3	X-RAY DIFFRACTION	3	A	157 - 192
4	X-RAY DIFFRACTION	4	A	193 - 211
5	X-RAY DIFFRACTION	5	B	2 - 76
6	X-RAY DIFFRACTION	6	B	77 - 108
7	X-RAY DIFFRACTION	7	B	109 - 146
8	X-RAY DIFFRACTION	8	B	147 - 211
9	X-RAY DIFFRACTION	9	C	2 - 35
10	X-RAY DIFFRACTION	10	C	36 - 56
11	X-RAY DIFFRACTION	11	C	57 - 162
12	X-RAY DIFFRACTION	12	C	163 - 211
13	X-RAY DIFFRACTION	13	D	2 - 75
14	X-RAY DIFFRACTION	14	D	76 - 159
15	X-RAY DIFFRACTION	15	D	160 - 187
16	X-RAY DIFFRACTION	16	D	188 - 211

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