PDB-3trf: Structure of a shikimate kinase (aroK) from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 3trf

Title

Structure of a shikimate kinase (aroK) from Coxiella burnetii

Components

Shikimate kinase

Keywords

TRANSFERASE / Amino acid biosynthesis

Function / homology

Function and homology information

shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6 Å

Authors

Cheung, J. / Franklin, M. / 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 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 27, 2016	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	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 / pdbx_struct_special_symmetry / 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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PDBx/mmCIF format	3trf.cif.gz	150.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3trf_validation.pdf.gz	447.1 KB	Display	wwPDB validaton report
Full document	3trf_full_validation.pdf.gz	449.5 KB	Display
Data in XML	3trf_validation.xml.gz	15 KB	Display
Data in CIF	3trf_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/3trf ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3trf	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 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C 1kagS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3dne-d 6y8c-d 2cpk-d 2gfc-d 2uw0-d 4ie9-d 4yxr-d 1xh4-d 3agm-d 3nx8-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Shikimate kinase

B: Shikimate kinase

hetero molecules

42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Shikimate kinase

hetero molecules

A: Shikimate kinase

hetero molecules

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

2

B: Shikimate kinase

hetero molecules

B: Shikimate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	98.429, 98.429, 157.071
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	B-62- ARG

#1: Protein	Shikimate kinase / SK Mass: 21157.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: aroK, CBU_1892 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AJ3, shikimate kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.5 Å³/Da / Density % sol: 50.83 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 0.2 M potassium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Jul 28, 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

Resolution: 2.3→50 Å / Num. all: 20758 / Num. obs: 20447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / R_merge(I) obs: 0.061 / Net I/σ(I): 10.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.3-2.34	8.5	0.39	1	92.6
2.34-2.38	9.9	0.368	1	94.4
2.38-2.43	10.7	0.318	1	98.3
2.43-2.48	12.2	0.323	1	99.9
2.48-2.53	13.4	0.264	1	100
2.53-2.59	13.8	0.211	1	100
2.59-2.66	14.3	0.211	1	100
2.66-2.73	14.4	0.176	1	100
2.73-2.81	14.2	0.15	1	100
2.81-2.9	14.2	0.123	1	100
2.9-3	14.4	0.115	1	100
3-3.12	14.2	0.093	1	100
3.12-3.26	14.2	0.075	1	100
3.26-3.44	14.2	0.065	1	100
3.44-3.65	14	0.058	1	100
3.65-3.93	14	0.051	1	99.9
3.93-4.33	13.9	0.048	1	99.8
4.33-4.95	13.5	0.045	1	99.6
4.95-6.24	13.4	0.045	1	99.6
6.24-50	11.5	0.042	1	87.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KAG

1kag

Resolution: 2.6→41.703 Å / Occupancy max: 1 / Occupancy min: 0.8 / SU ML: 0.41 / σ(F): 0 / Phase error: 27.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2702	728	5.09 %
R_work	0.2055	-	-
obs	0.2087	14293	98.89 %
all	-	15189	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 57.6 Å² / k_sol: 0.347 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.447 Å²	0 Å²	0 Å²
2-	-	-6.447 Å²	0 Å²
3-	-	-	12.894 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→41.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2681	0	10	84	2775

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2727
X-RAY DIFFRACTION	f_angle_d	0.702	3662
X-RAY DIFFRACTION	f_dihedral_angle_d	13.915	1078
X-RAY DIFFRACTION	f_chiral_restr	0.05	420
X-RAY DIFFRACTION	f_plane_restr	0.002	470

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.8007	0.3593	159	0.2801	2646	X-RAY DIFFRACTION	100
2.8007-3.0825	0.3483	147	0.2626	2673	X-RAY DIFFRACTION	100
3.0825-3.5284	0.2934	162	0.2055	2681	X-RAY DIFFRACTION	100
3.5284-4.4446	0.2436	126	0.1826	2766	X-RAY DIFFRACTION	100
4.4446-41.7081	0.2248	134	0.1909	2799	X-RAY DIFFRACTION	95

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	0.1352	0.0137	0.0602	0.3055	-0.1597	0.1238	-0.1688	-0.1402	-0.1648	0.1361	-0.0108	0.2633	-0.1662	0.0105	-0.0007	0.3982	0.1076	0.1589	0.3394	0.1028	0.4593	31.2729	25.6721	-1.8384
2	0.0392	0.0152	0.0347	0.0245	0.0309	0.3336	-0.1519	-0.0023	-0.018	0.1333	-0.1745	0.1871	-0.0206	-0.0589	0.1796	0.4433	0.0817	0.0171	0.3744	0.0221	0.7237	29.8637	23.4373	-14.6665
3	0.2249	-0.222	0.0728	0.5106	0.0185	0.1119	-0.0366	0.1161	-0.121	-0.0122	0.0342	0.4177	-0.0313	-0.0675	-0.1622	0.3646	0.1571	-0.1358	0.2206	-0.0013	0.4483	30.9226	33.4116	-20.6843
4	0.192	-0.0319	0.101	0.0099	-0.0182	0.33	-0.166	-0.0854	0.0284	0.0193	-0.0295	0.3073	-0.1045	-0.1871	-0.1504	0.3315	0.2059	0.2015	0.2769	0.0115	0.6786	26.0691	34.3163	-6.3267
5	0.2744	-0.1094	0.0224	0.3992	-0.0255	0.0041	-0.0462	-0.143	0.1057	-0.0154	-0.1032	-0.1419	-0.0762	0.0178	0.0225	0.2862	0.1053	-0.061	0.2639	0.0813	0.2688	51.0137	26.243	-6.6183
6	0.4617	-0.2617	0.105	0.1509	-0.0148	0.7843	-0.3413	-0.3292	0.0745	0.3159	0.1211	-0.115	-0.1894	0.2207	-0.0457	0.5201	0.165	-0.0106	0.2579	-0.0215	0.2959	37.2615	33.7549	1.4253
7	0.1395	0.009	-0.0941	0.0645	0.0335	0.0956	-0.1433	-0.0582	0.0677	0.1434	-0.1092	-0.1567	-0.0312	0.0973	-0.1732	0.4403	0.127	-0.1677	0.3082	-0.0331	0.2567	29.7273	67.673	-1.7852
8	0.2695	-0.1304	-0.3115	0.3681	0.4152	0.6285	-0.0443	0.0714	-0.0603	0.114	-0.0921	-0.1002	-0.0879	-0.1096	0.0363	0.4669	0.1595	0.0919	0.3965	0.0061	0.308	29.475	67.0183	-17.1354
9	0.2369	-0.0015	-0.1048	0.28	0.0736	0.5089	-0.1816	0.2229	-0.1638	-0.1725	-0.1885	-0.2998	0.0817	-0.0942	-0.7238	0.2135	0.3789	0.0986	0.07	-0.305	0.3103	31.296	59.9524	-17.3273
10	0.2139	-0.0958	-0.0028	0.3939	-0.1084	0.209	-0.1377	-0.107	-0.146	0.3754	0.0391	-0.1146	0.1084	-0.0782	-0.1087	0.3843	0.1386	0.0028	0.2049	0.0384	0.2669	27.1046	56.9195	-4.7589
11	0.3601	-0.169	0.0104	0.1579	-0.1478	0.2594	0.0835	-0.0374	-0.2067	-0.2103	-0.0926	0.1876	0.1317	0.0374	0.0268	0.5121	0.0721	0.0841	0.2877	-0.0895	0.4376	7.1717	69.0566	-9.8609
12	0.0113	-0.0462	-0.0245	0.3821	0.0679	0.0714	-0.1416	-0.0306	-0.0902	0.1445	-0.0645	0.2898	0.1154	-0.0767	-0.211	0.5724	0.1445	0.2927	0.1441	0.117	0.6687	18.0635	50.517	-5.538
13	-0.0001	0.0053	-0.0013	0.0797	0.0022	-0.0003	-0.0149	-0.1321	0.1	0.2154	0.0794	0.0285	-0.2313	-0.2841	-0.001	0.9759	0.2501	-0.1537	0.5664	0.0166	0.2557	27.2691	65.3481	7.752

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:29)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 30:47)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 48:73)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 74:105)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 106:128)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 129:174)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 6:32)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 33:47)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 48:82)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 83:116)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 117:128)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 129:149)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 150:173)

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