PDB-3vav: Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 3vav

Title

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia thailandensis

Components

3-methyl-2-oxobutanoate hydroxymethyltransferase

Keywords

TRANSFERASE /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Burkolderia thailandensis /

melioidosis / Ketopantoate hydroxymethyltransferase (KPHMT)

Function / homology

Function and homology information

3-methyl-2-oxobutanoate hydroxymethyltransferase /

3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...

History

Deposition	Dec 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3vav.cif.gz	936.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3vav.ent.gz	775.5 KB	Display	PDB format
PDBx/mmJSON format	3vav.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/va/3vav ftp://data.pdbj.org/pub/pdb/validation_reports/va/3vav	HTTPS FTP

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Related structure data

Related structure data	3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3f0fC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8C 3t4cC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 4ddoC 4dfeC 4dheC 4dhkC 4dutC 4dz4C 4e4tC 4efiC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4ghkC 4h3yC 4h3zC 4h4gC 3ez4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ez4-d 1oy0-1 1o68-2 1m3u-d 6whg-d 1glb-1 1flo-d 1wx0-d 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: ButhA.00112.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (2)

Deposited unit

A: 3-methyl-2-oxobutanoate hydroxymethyltransferase

B: 3-methyl-2-oxobutanoate hydroxymethyltransferase

C: 3-methyl-2-oxobutanoate hydroxymethyltransferase

D: 3-methyl-2-oxobutanoate hydroxymethyltransferase

E: 3-methyl-2-oxobutanoate hydroxymethyltransferase

F: 3-methyl-2-oxobutanoate hydroxymethyltransferase

G: 3-methyl-2-oxobutanoate hydroxymethyltransferase

H: 3-methyl-2-oxobutanoate hydroxymethyltransferase

I: 3-methyl-2-oxobutanoate hydroxymethyltransferase

J: 3-methyl-2-oxobutanoate hydroxymethyltransferase

hetero molecules

291 kDa, 10 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)	81.710, 174.750, 104.580
Angle α, β, γ (deg.)	90.000, 108.710, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-methyl-2-oxobutanoate hydroxymethyltransferase / / Ketopantoate hydroxymethyltransferase / KPHMT Mass: 29052.336 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1311, panB / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) References: UniProt: Q2SYZ1, 3-methyl-2-oxobutanoate hydroxymethyltransferase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2458 / 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: 2.43 Å³/Da / Density % sol: 49.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: ButhA.00112.a.A1 PW33325 at 38.6 mg/mL against PACT H2 0.2 M sodium bromide, 0.1 M Bis Tris propane pH 8.5, 20% PEG 3350, crystal tracking ID 225054h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 256134 / Num. obs: 255864 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / B_iso Wilson estimate: 22.655 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 23.86

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	Num. unique obs	% possible all
1.8-1.85		7.1	0.452	4.31	133976	18885	18851	99.8
1.85-1.9			0.365	5.37	133063		18492	99.9
1.9-1.95			0.287	6.82	130045		17845	99.9
1.95-2.01			0.235	8.34	128212		17398	99.9
2.01-2.08			0.196	10.03	125441		16866	100
2.08-2.15			0.16	12.27	122246		16339	99.9
2.15-2.23			0.136	14.46	118243		15719	99.9
2.23-2.32			0.114	17	114572		15200	99.9
2.32-2.43			0.104	18.63	109314		14492	100
2.43-2.55			0.088	21.8	105199		13942	99.9
2.55-2.68			0.076	24.92	99681		13226	100
2.68-2.85			0.064	29.28	93861		12466	99.9
2.85-3.04			0.054	33.87	88596		11772	99.9
3.04-3.29			0.042	42.39	82044		10954	99.9
3.29-3.6			0.033	53.18	74628		10069	99.9
3.6-4.02			0.029	59.82	66361		9131	99.9
4.02-4.65			0.024	68.08	59012		8051	99.9
4.65-5.69			0.024	65.9	52258		6825	99.9
5.69-8.05			0.024	64.67	40749		5313	99.8
	8.05		0.016	84.94	21985		2913	99.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	47.83 Å
Translation	3 Å	47.83 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3ez4

3ez4

Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.1635 / WR_factor R_work: 0.1431 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9214 / SU B: 3.756 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0221 / SU R_free: 0.0208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1801	12850	5 %	RANDOM
R_work	0.1537	-	-	-
obs	0.155	255850	99.86 %	-
all	-	256134	-	-

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 max: 70.67 Å² / B_iso mean: 18.1463 Å² / B_iso min: 6.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.88 Å²	0 Å²	0.49 Å²
2-	-	2.19 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18653	0	45	2458	21156

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	19502
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12905
X-RAY DIFFRACTION	r_angle_refined_deg	1.326	1.97	26605
X-RAY DIFFRACTION	r_angle_other_deg	0.904	3	31546
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.953	5	2629
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.163	23.55	783
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.004	15	3005
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.491	15	143
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3127
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	22216
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3935

LS refinement shell

Resolution: 1.799→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.228	939	-
R_work	0.195	17592	-
all	-	18531	-
obs	-	-	98.32 %

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	0.2877	0.0071	-0.1183	0.2779	-0.1395	0.2459	-0.0188	-0.017	0.0246	0.0279	-0.0048	-0.003	0.0034	-0.0043	0.0236	0.049	-0.0085	-0.0081	0.0603	0.0165	0.0725	-2.8677	38.0022	7.4844
2	0.5357	0.2633	-0.3202	0.2655	-0.3212	0.4869	-0.0266	0.0678	0.0303	-0.0444	0.027	0.0228	0.0161	-0.0543	-0.0004	0.0342	-0.0064	-0.0174	0.0652	0.0338	0.0836	-6.5106	43.9821	-7.3781
3	0.2949	-0.1681	-0.1209	0.2118	0.1731	0.1842	0.0119	0.0512	0.0338	0.0179	-0.0195	0.0331	0.0049	0.0108	0.0076	0.0378	0.0009	-0.0012	0.0894	0.013	0.0657	-3.8635	9.0419	-5.047
4	0.9041	-0.266	-0.4863	0.4795	0.3306	0.4756	-0.0287	0.14	-0.1008	-0.0277	-0.0692	0.0721	0.0278	-0.0808	0.0979	0.0177	0.0043	-0.0085	0.1302	-0.0255	0.0463	-8.6915	-1.3751	-15.7737
5	0.391	-0.0933	0.0915	0.3808	-0.0465	0.0472	-0.0031	0.0441	-0.0221	0.0097	0.0048	0.0179	-0.0182	0.0063	-0.0017	0.0405	0.0012	-0.0012	0.0792	-0.0103	0.0616	-8.4849	-10.7725	18.4075
6	0.8007	-0.5484	0.1475	0.8712	-0.1679	0.1634	-0.0074	-0.0702	-0.1055	0.0434	0.026	0.1129	0.032	-0.0265	-0.0187	0.0194	-0.0151	-0.0038	0.0697	-0.0007	0.0922	-15.714	-22.8973	25.4908
7	0.3333	0.0215	0.1633	0.0431	-0.0393	0.2893	0.0085	-0.0257	-0.0213	-0.0047	-0.0094	0.012	-0.0111	-0.0134	0.0009	0.0488	0.0044	0.0111	0.0884	0.0004	0.0511	-10.6757	5.4033	44.966
8	0.8508	-0.265	0.39	0.2223	-0.0222	0.8819	-0.0383	-0.1649	0.0676	0.0621	0.0292	0.0447	-0.0321	-0.1018	0.0091	0.024	0.0052	0.0264	0.1418	-0.0147	0.0443	-17.4364	8.9748	58.8121
9	0.3694	0.1139	0.1129	0.302	0.049	0.1419	-0.0416	-0.0291	0.0141	0.0156	0.05	0.0304	-0.0301	-0.0253	-0.0084	0.075	0.0183	0.0034	0.0575	-0.0098	0.0596	-7.4961	35.9256	37.7954
10	0.9648	0.2785	0.6471	0.7564	0.188	0.6049	-0.1917	0.0336	0.2184	0.0245	0.0808	0.1507	-0.195	-0.0293	0.1109	0.0905	0.0405	-0.0378	0.0507	-0.0078	0.1257	-11.9249	51.2508	37.9628
11	0.3205	-0.1755	0.0722	0.2135	-0.1778	0.1971	0.0086	0.0504	0.0111	0.0154	-0.0164	-0.0078	-0.0066	0.0236	0.0078	0.0432	-0.0079	-0.0062	0.0794	0.0225	0.0716	27.6347	28.8311	3.2249
12	1.0174	-0.3544	0.5399	0.5837	-0.4189	0.4912	-0.0615	0.078	0.1942	0.0309	-0.0299	-0.0963	-0.0499	0.0706	0.0914	0.0101	-0.0222	-0.0138	0.077	0.06	0.1188	35.0916	42.368	-0.4472
13	0.3213	-0.05	0.1239	0.0926	0.0688	0.3044	-0.0009	0.0121	-0.0131	0.0071	-0.017	-0.0032	0.0055	0.0135	0.0179	0.0472	0.0006	0.0033	0.085	0.009	0.0512	25.3722	-2.2382	3.1696
14	0.6042	0.1301	0.1421	0.0906	0.1678	0.6606	-0.0036	0.1296	0.0085	-0.0246	0.0058	-0.0305	0.0088	0.0769	-0.0021	0.0277	0.024	0.0214	0.127	0.0137	0.0385	33.1537	-2.8828	-10.3736
15	0.2876	0.0818	0.0924	0.3076	0.0455	0.0575	0.0052	-0.0126	-0.0186	0.007	0.005	-0.0063	-0.0136	0.0066	-0.0102	0.052	-0.002	-0.0021	0.0745	0.0055	0.0572	20.7644	-11.8714	32.3917
16	0.5221	0.3127	-0.0167	0.5596	0.0959	0.1885	-0.0043	0.0498	-0.1191	-0.0058	0.0322	-0.0859	0.0212	0.0139	-0.0279	0.0323	0.011	-0.0169	0.059	-0.0021	0.0937	25.5946	-26.5014	28.0788
17	0.4963	0.0875	-0.1729	0.0501	-0.0018	0.2767	-0.0004	-0.0622	0.0537	-0.0222	0.0015	-0.0157	0.0156	0.0027	-0.0011	0.0475	-0.0004	0.0013	0.0886	-0.0152	0.0525	20.1594	13.413	51.1154
18	0.8991	-0.1774	-0.3597	0.349	-0.2149	0.4171	-0.0443	-0.2088	-0.0475	-0.0016	0.033	0.0026	0.0392	0.0741	0.0112	0.016	0.0047	-0.0116	0.1551	0.015	0.0183	23.4625	4.1828	63.5331
19	0.187	-0.0786	-0.0393	0.2219	0.1645	0.296	-0.0283	0.0091	0.0086	-0.0056	0.0067	0.01	-0.0348	0.0405	0.0216	0.0801	-0.0213	-0.0134	0.0519	-0.008	0.0566	24.4279	38.4421	32.9159
20	0.4406	-0.4073	-0.1103	0.6318	0.4381	0.5121	-0.0863	-0.0622	0.0426	0.0498	0.0814	-0.0414	-0.0707	0.078	0.0049	0.0879	-0.0285	-0.0332	0.0581	-0.029	0.0655	29.0934	46.7797	45.75

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 146
2	X-RAY DIFFRACTION	2	A	165 - 271
3	X-RAY DIFFRACTION	3	B	10 - 147
4	X-RAY DIFFRACTION	4	B	167 - 270
5	X-RAY DIFFRACTION	5	C	9 - 147
6	X-RAY DIFFRACTION	6	C	167 - 271
7	X-RAY DIFFRACTION	7	D	9 - 146
8	X-RAY DIFFRACTION	8	D	167 - 271
9	X-RAY DIFFRACTION	9	E	9 - 146
10	X-RAY DIFFRACTION	10	E	166 - 271
11	X-RAY DIFFRACTION	11	F	9 - 146
12	X-RAY DIFFRACTION	12	F	165 - 271
13	X-RAY DIFFRACTION	13	G	9 - 147
14	X-RAY DIFFRACTION	14	G	168 - 271
15	X-RAY DIFFRACTION	15	H	9 - 147
16	X-RAY DIFFRACTION	16	H	164 - 271
17	X-RAY DIFFRACTION	17	I	9 - 147
18	X-RAY DIFFRACTION	18	I	165 - 271
19	X-RAY DIFFRACTION	19	J	10 - 146
20	X-RAY DIFFRACTION	20	J	164 - 271

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