PDB-2h34: Apoenzyme crystal structure of the tuberculosis serine/threonine ...

ID or keywords:

Entry

Database: PDB / ID: 2h34

Title

Apoenzyme crystal structure of the tuberculosis serine/threonine kinase, PknE

Components

Serine/threonine-protein kinase pknE

Keywords

TRANSFERASE /

apoenzyme /

serine/threonine protein kinase

Function / homology

Function and homology information

response to nitrosative stress / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / positive regulation of catalytic activity / : / protein autophosphorylation / membrane => GO:0016020 /

non-specific serine/threonine protein kinase /

protein kinase activity /

protein phosphorylation ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Gay, L.M. / Ng, H.L. / Alber, T.

Citation

Journal: J.Mol.Biol. / Year: 2006
Title: A Conserved Dimer and Global Conformational Changes in the Structure of apo-PknE Ser/Thr Protein Kinase from Mycobacterium tuberculosis.
Authors: Gay, L.M. / Ng, H.L. / Alber, T.

History

Deposition	May 22, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2h34.cif.gz	102.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/2h34 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/2h34	HTTPS FTP

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Related structure data

Similar structure data	2og8-1 4csv-d 1vl5-1 3efw-2 1j6r-2 2v5g-1 3tx4-2 7a11-1 4g34-d 1xxl-1 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
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Serine/threonine-protein kinase pknE

B: Serine/threonine-protein kinase pknE

hetero molecules

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

1

A: Serine/threonine-protein kinase pknE

hetero molecules

defined by author
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serine/threonine-protein kinase pknE

hetero molecules

defined by author
34.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.078, 77.078, 221.024
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

Details

The biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B)

#1: Protein	Serine/threonine-protein kinase pknE Mass: 34058.152 Da / Num. of mol.: 2 / Fragment: phosphotransfer catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pknE / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P72001, UniProt: P9WI77*PLUS, non-specific serine/threonine protein kinase
#2: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.781035 Å³/Da / Density % sol: 55.771862 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 7 Details: 12% PEG 8000, 0.2M NaBr, 0.1M HEPES pH 7.0, microbatch, temperature 291K

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Data collection

Diffraction

Mean temperature: 93 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 0.9796 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2004

Radiation

Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9796 Å / Relative weight: 1

Reflection

Redundancy: 5.8 % / Av σ(I) over netI: 12.3 / Number: 106124 / R_merge(I) obs: 0.088 / Χ²: 2.82 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 18268 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.03	50	99.2	1	0.074	13.28	5.6
4.79	6.03	100	1	0.07	4.678	5.8
4.18	4.79	100	1	0.061	2.641	5.9
3.8	4.18	100	1	0.071	1.878	5.8
3.53	3.8	100	1	0.09	1.486	5.8
3.32	3.53	100	1	0.133	1.107	5.8
3.15	3.32	100	1	0.197	0.954	5.8
3.02	3.15	100	1	0.289	0.816	5.8
2.9	3.02	100	1	0.408	0.795	5.8
2.8	2.9	100	1	0.615	0.755	5.8

Reflection

Resolution: 2.8→50 Å / Num. obs: 18268 / % possible obs: 99.9 % / Redundancy: 5.8 % / R_merge(I) obs: 0.088 / Χ²: 2.816 / Net I/σ(I): 12.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.9	5.8	0.615	1819	0.755	1	100
2.9-3.02	5.8	0.408	1807	0.795	1	100
3.02-3.15	5.8	0.289	1830	0.816	1	100
3.15-3.32	5.8	0.197	1819	0.954	1	100
3.32-3.53	5.8	0.133	1827	1.107	1	100
3.53-3.8	5.8	0.09	1827	1.486	1	100
3.8-4.18	5.8	0.071	1822	1.878	1	100
4.18-4.79	5.9	0.061	1838	2.641	1	100
4.79-6.03	5.8	0.07	1830	4.678	1	100
6.03-50	5.6	0.074	1849	13.28	1	99.2

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.8 Å / D res low: 50 Å / FOM : 0.34 / Reflection: 17500

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.559	0.02	0.166	1.43
2	Se	60	0.428	0.659	0.036	1.329
3	Se	60	0.918	0.376	0.166	1.465
4	Se	60	0.027	0.662	0.141	1.309
5	Se	60	0.593	0.385	0.054	1.151
6	Se	60	0.311	0.236	0.083	1.168
7	Se	60	0.225	0.969	0.049	1.182
8	Se	60	0.404	0.554	0.041	0.969
9	Se	60	0.206	0.809	0.075	0.71
10	Se	60	0.402	0.697	0.027	1.048
11	Se	60	0.39	0.787	0.034	0.842
12	Se	60	0.147	0.804	0.087	0.839
13	Se	60	0.162	0.842	0.073	0.782
14	Se	60	0.216	0.274	0.096	0.497
15	Se	60	0.208	0.34	0.081	0.593
16	Se	60	0.17	0.282	0.103	0.479

Phasing MAD shell

Resolution (Å)	FOM	Reflection
10.1-50	0.52	830
6.37-10.1	0.57	1481
4.98-6.37	0.49	1907
4.22-4.98	0.44	2251
3.73-4.22	0.37	2523
3.37-3.73	0.29	2746
3.1-3.37	0.22	2872
2.89-3.1	0.14	2890

Phasing dm

FOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.64 / Reflection: 17501 / Reflection acentric: 17178 / Reflection centric: 323

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8-34.149	0.97	0.97	0.95	787	747	40
5-8	0.91	0.91	0.78	2423	2357	66
4-5	0.86	0.86	0.7	3043	2982	61
3.5-4	0.75	0.75	0.67	3012	2965	47
3-3.5	0.45	0.45	0.47	5251	5180	71
2.8-3	0.23	0.23	0.27	2985	2947	38

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.06	phasing
RESOLVE	2.06	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	2	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.8→34.1 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.894 / WR_factor R_free: 0.266 / WR_factor R_work: 0.217 / SU B: 34.573 / SU ML: 0.309 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.824 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.265	908	5.2 %	RANDOM
R_work	0.216	-	-	-
all	0.218	-	-	-
obs	0.218	17499	100 %	-

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: 74.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	-0.16 Å²	0 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	0.48 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→34.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3642	0	3	0	3645

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3707
X-RAY DIFFRACTION	r_angle_refined_deg	1.208	1.976	5042
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.104	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.204	22.956	159
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.599	15	560
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.808	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	573
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2857
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	1751
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	2536
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	125
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.284	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	0.488	1.5	2410
X-RAY DIFFRACTION	r_mcangle_it	0.949	2	3844
X-RAY DIFFRACTION	r_scbond_it	1.73	3	1319
X-RAY DIFFRACTION	r_scangle_it	2.722	4.5	1198

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.8-2.873	0.314	62	0.287	1081	1143
2.873-2.951	0.319	72	0.262	1071	1143
2.951-3.036	0.276	63	0.235	1109	1172
3.036-3.129	0.292	65	0.249	1078	1143
3.129-3.231	0.306	60	0.237	1089	1149
3.231-3.343	0.29	67	0.227	1063	1130
3.343-3.468	0.297	56	0.228	992	1048
3.468-3.608	0.211	56	0.187	1019	1075
3.608-3.766	0.221	55	0.212	950	1005
3.766-3.948	0.322	47	0.216	935	982
3.948-4.158	0.257	44	0.199	899	943
4.158-4.407	0.248	42	0.206	825	867
4.407-4.705	0.309	35	0.186	809	844
4.705-5.074	0.27	33	0.2	756	789
5.074-5.546	0.222	38	0.224	678	716
5.546-6.18	0.245	27	0.259	619	646
6.18-7.098	0.301	34	0.231	553	587
7.098-8.6	0.227	20	0.202	476	496
8.6-11.793	0.221	21	0.159	358	379
11.793-34.1	0.263	11	0.282	231	242

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	2.477	-0.4095	-0.1316	4.7689	-2.5168	2.3269	0.5644	-0.9821	0.5417	0.9979	-0.3903	1.182	-1.0035	-0.7901	-0.1741	0.1788	-0.036	0.228	0.3716	-0.232	0.0821	11.468	14.596	21.822
2	3.039	-0.2296	1.24	7.2506	0.6601	4.0933	-0.049	0.1075	0.2151	-0.2792	-0.2975	-0.2821	-0.6582	-0.1086	0.3465	0.0004	0.3302	-0.0638	-0.3569	0.0221	-0.248	20.503	31.234	3.326
3	6.805	0.9127	-0.3743	5.9631	-1.7977	3.5755	0.3343	-0.6279	-1.3149	0.0393	-0.5942	0.6329	0.7747	-0.5856	0.26	-0.0278	-0.0836	0.0502	0.0367	0.0579	0.0293	15.498	-4.661	14.323
4	5.8935	-1.3139	0.0537	6.0386	2.8071	4.4873	0.3176	0.5907	0.0933	-0.1526	0.0232	-0.5505	0.2752	0.4411	-0.3409	-0.1376	0.3015	0.0098	-0.3006	0.1033	-0.2254	38.708	-2.509	1.75

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	14 - 100	34 - 120
2	2	A	A	101 - 276	121 - 296
3	3	B	B	14 - 100	34 - 120
4	4	B	B	101 - 276	121 - 296

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