PDB-3tr1: Structure of a 3-phosphoshikimate 1-carboxyvinyltransferase (aroA...

ID or keywords:

Entry

Database: PDB / ID: 3tr1

Title

Structure of a 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) from Coxiella burnetii

Components

3-phosphoshikimate 1-carboxyvinyltransferase

EPSP synthase

Keywords

TRANSFERASE / Amino acid biosynthesis

Function / homology

Function and homology information

3-phosphoshikimate 1-carboxyvinyltransferase /

3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process /

cytoplasm
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Oct 21, 2015	Group: Database references
Revision 1.3	Feb 10, 2016	Group: Database references
Revision 1.4	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tr1.cif.gz	180.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3tr1.ent.gz	150.1 KB	Display	PDB format
PDBx/mmJSON format	3tr1.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/tr/3tr1 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3tr1	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	4egr-3 5wxv-1 3slh-4 1mi4-d 4egr-6 2qft-d 4egr-2 4egr-5 2pq9-d 3g7u-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#218 - Feb 2018 EPSP Synthase and Weedkillers similarity (9)

Deposited unit

A: 3-phosphoshikimate 1-carboxyvinyltransferase

hetero molecules

48 kDa, 1 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)	94.026, 94.026, 233.086
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	3-phosphoshikimate 1-carboxyvinyltransferase / EPSP synthase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS Mass: 47440.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: aroA, CBU_0526 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83E11, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.13 Å³/Da / Density % sol: 60.76 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.1M glycine pH 10.5, 0.2M lithium sulfate, 1.2M sodium hydrogen phosphate, 0.8M potassium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4C / Wavelength: 0.979 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2011

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Redundancy: 4.6 % / Av σ(I) over netI: 21.96 / Number: 351355 / R_merge(I) obs: 0.083 / Χ²: 1.44 / D res high: 2 Å / D res low: 30 Å / Num. obs: 76948 / % possible obs: 98.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.42	30	91.8	1	0.052	3.284	4.6
4.31	5.42	96.9	1	0.063	3.757	4.7
3.76	4.31	95.9	1	0.066	3.512	4.7
3.42	3.76	96.8	1	0.073	3.071	4.7
3.17	3.42	97.8	1	0.082	2.576	4.8
2.99	3.17	98.2	1	0.093	2.044	4.8
2.84	2.99	98.9	1	0.103	1.661	4.7
2.71	2.84	99.6	1	0.114	1.301	4.7
2.61	2.71	99.7	1	0.128	1.063	4.7
2.52	2.61	99.4	1	0.135	0.935	4.7
2.44	2.52	99.5	1	0.158	0.788	4.7
2.37	2.44	99.6	1	0.168	0.706	4.7
2.31	2.37	99.6	1	0.195	0.608	4.6
2.25	2.31	99.6	1	0.226	0.551	4.6
2.2	2.25	99.5	1	0.242	0.485	4.6
2.15	2.2	99.7	1	0.312	0.433	4.6
2.11	2.15	99.8	1	0.334	0.399	4.6
2.07	2.11	99.3	1	0.392	0.368	4.4
2.03	2.07	97.9	1	0.427	0.36	4
2	2.03	95.7	1	0.481	0.344	3.4

Reflection

Resolution: 2→30 Å / Num. all: 78278 / Num. obs: 76948 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / R_merge(I) obs: 0.083 / Χ²: 1.439 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.03	3.4	0.481	3741	0.344	1	95.7
2.03-2.07	4	0.427	3799	0.36	1	97.9
2.07-2.11	4.4	0.392	3900	0.368	1	99.3
2.11-2.15	4.6	0.334	3915	0.399	1	99.8
2.15-2.2	4.6	0.312	3914	0.433	1	99.7
2.2-2.25	4.6	0.242	3869	0.485	1	99.5
2.25-2.31	4.6	0.226	3922	0.551	1	99.6
2.31-2.37	4.6	0.195	3900	0.608	1	99.6
2.37-2.44	4.7	0.168	3867	0.706	1	99.6
2.44-2.52	4.7	0.158	3911	0.788	1	99.5
2.52-2.61	4.7	0.135	3898	0.935	1	99.4
2.61-2.71	4.7	0.128	3890	1.063	1	99.7
2.71-2.84	4.7	0.114	3901	1.301	1	99.6
2.84-2.99	4.7	0.103	3862	1.661	1	98.9
2.99-3.17	4.8	0.093	3850	2.044	1	98.2
3.17-3.42	4.8	0.082	3833	2.576	1	97.8
3.42-3.76	4.7	0.073	3794	3.071	1	96.8
3.76-4.31	4.7	0.066	3767	3.512	1	95.9
4.31-5.42	4.7	0.063	3791	3.757	1	96.9
5.42-30	4.6	0.052	3624	3.284	1	91.8

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2→29.947 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8847 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR phasing

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1949	2124	5.07 %	RANDOM
R_work	0.1784	-	-	-
obs	0.1793	41927	99.11 %	-
all	-	44446	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.853 Å² / k_sol: 0.331 e/Å³

Displacement parameters

B_iso max: 287.78 Å² / B_iso mean: 43.7512 Å² / B_iso min: 20.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7355 Å²	0 Å²	-0 Å²
2-	-	0.7355 Å²	-0 Å²
3-	-	-	-1.471 Å²

Refinement step

Cycle: LAST / Resolution: 2→29.947 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3234	0	26	276	3536

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3302
X-RAY DIFFRACTION	f_angle_d	1.07	4475
X-RAY DIFFRACTION	f_chiral_restr	0.073	530
X-RAY DIFFRACTION	f_plane_restr	0.004	582
X-RAY DIFFRACTION	f_dihedral_angle_d	12.138	1230

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0675	0.2952	206	0.2391	3835	4041	98
2.0675-2.1502	0.1908	212	0.1951	3915	4127	100
2.1502-2.248	0.2448	204	0.1882	3938	4142	100
2.248-2.3665	0.2214	206	0.1905	3964	4170	100
2.3665-2.5147	0.2026	195	0.1873	3964	4159	100
2.5147-2.7088	0.2088	227	0.1918	3968	4195	100
2.7088-2.9811	0.2159	223	0.1866	3967	4190	100
2.9811-3.412	0.2095	236	0.1877	3996	4232	99
3.412-4.2967	0.177	204	0.1608	4074	4278	99
4.2967-29.95	0.1621	211	0.1669	4182	4393	96

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	1.6985	0.3249	0.7052	0.7242	-0.1124	0.4405	0.0629	-0.1216	-0.1524	0.0271	-0.047	0.1407	-0.0463	-0.196	-0.0233	0.1467	0.0205	-0.0124	0.3399	0.0249	0.2302	42.6066	46.6099	1.6604
2	1.8803	0.2051	1.2166	1.173	0.3485	0.9433	0.196	-0.9121	0.0357	0.2782	-0.1362	-0.1265	0.0524	-0.3342	-0.0333	0.2494	-0.0585	0.01	0.7061	0.0594	0.2325	39.1269	42.551	21.1758
3	4.1663	-0.335	-4.0885	0.714	-0.0032	4.3944	0.0855	-1	0.0939	0.5068	-0.0636	0.3178	-0.2085	0.0938	-0.0242	0.3503	0.0586	0.0264	0.7404	-0.116	0.3221	35.4465	54.6928	22.5301
4	0.1083	0.1599	-0.235	1.0476	0.9621	2.5631	0.094	-0.442	0.3641	0.0028	-0.1696	0.2452	-0.4862	-0.2832	0.1314	0.3002	0.0862	0.0278	0.5951	-0.1095	0.4329	34.8685	61.3284	12.642
5	0.9838	-0.1982	-0.0252	0.4158	-0.2776	1.3511	0.0175	0.0642	0.3579	0.0333	-0.0778	0.052	-0.5019	0.003	0.0559	0.3192	-0.0014	-0.0112	0.3156	0.0457	0.4091	56.6473	64.1696	1.7051
6	0.6763	-0.0875	-0.904	0.5184	0.2147	2.14	0.1182	-0.0999	0.4495	-0.1234	0.0278	-0.2496	-0.251	0.5885	-0.1255	0.3387	-0.1007	-0.0055	0.3809	0.0554	0.4712	71.4418	66.6859	5.0829
7	0.3858	0.062	-0.0592	1.0153	0.3741	1.127	0.0172	-0.0192	-0.0684	0.0759	-0.0735	-0.0545	-0.0492	0.0831	0.0561	0.1673	-0.0407	-0.0321	0.3503	0.0228	0.2577	66.4294	52.1236	13.3272
8	0.5502	0.1078	-0.7087	0.7769	-0.1307	1.032	0.0923	0.4674	-0.3366	0.0806	-0.0925	-0.0198	0.0024	-0.3111	-0.026	0.1422	-0.0225	-0.034	0.382	0.0072	0.2872	61.2531	44.6413	-2.4117

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 0:94)	A	0 - 94
2	X-RAY DIFFRACTION	2	(chain A and resid 95:154)	A	95 - 154
3	X-RAY DIFFRACTION	3	(chain A and resid 155:182)	A	155 - 182
4	X-RAY DIFFRACTION	4	(chain A and resid 183:232)	A	183 - 232
5	X-RAY DIFFRACTION	5	(chain A and resid 233:295)	A	233 - 295
6	X-RAY DIFFRACTION	6	(chain A and resid 296:303)	A	296 - 303
7	X-RAY DIFFRACTION	7	(chain A and resid 304:408)	A	304 - 408
8	X-RAY DIFFRACTION	8	(chain A and resid 409:436)	A	409 - 436

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