PDB-3cwc: Crystal structure of putative glycerate kinase 2 from Salmonella ...

ID or keywords:

Entry

Database: PDB / ID: 3cwc

Title

Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2

Components

Putative glycerate kinase 2

Keywords

TRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / IDP122 / Kinase

Function / homology

Function and homology information

organic acid phosphorylation / glycerate 2-kinase activity / glycerate kinase activity
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.23 Å

Authors

Osipiuk, J. / Zhou, M. / Holzle, D. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: X-ray crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2.
Authors: Osipiuk, J. / Zhou, M. / Holzle, D. / Anderson, W. / Joachimiak, A.

History

Deposition	Apr 21, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Apr 2, 2014	Group: Source and taxonomy
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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	3cwc.cif.gz	150.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3cwc.ent.gz	119.3 KB	Display	PDB format
PDBx/mmJSON format	3cwc.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/cw/3cwc ftp://data.pdbj.org/pub/pdb/validation_reports/cw/3cwc	HTTPS FTP

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Related structure data

Related structure data	1to6 2b8n
Similar structure data	3zha-2 2p7m-4 2p7l-4 2p7q-4 1bg9-1 2p7p-4 3bry-d 1f0k-d 7bel-2 6tvp-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: APC23911MCSG target

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative glycerate kinase 2

B: Putative glycerate kinase 2

hetero molecules

80.5 kDa, 2 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)	63.733, 59.549, 103.605
Angle α, β, γ (deg.)	90.000, 106.010, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

#1: Protein	Putative glycerate kinase 2 Mass: 40152.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Strain: LT2 / Gene: STM2959 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZME0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.73 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 10% PEG 3000, 0.1 M Phosphate-citrate buffer, 0.2 M Sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2008
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.23→49.81 Å / Num. all: 36765 / Num. obs: 36765 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / B_iso Wilson estimate: 49.8 Å² / R_merge(I) obs: 0.075 / Net I/σ(I): 31.4
Reflection shell	Resolution: 2.23→2.27 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.622 / Mean I/σ(I) obs: 2.09 / Num. unique all: 1789 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.23→49.81 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.943 / SU B: 14.805 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.284 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Funded by the National Institute of Allergy and Infectious Diseases of NIH (Contract Number HHSN272200700058C).

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	1834	5 %	RANDOM
R_work	0.188	-	-	-
all	0.191	36722	-	-
obs	0.191	36722	99.6 %	-

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: 38.093 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	-1.21 Å²
2-	-	0.96 Å²	0 Å²
3-	-	-	-0.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.23→49.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5405	0	9	153	5567

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	5483
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3589
X-RAY DIFFRACTION	r_angle_refined_deg	1.547	1.969	7429
X-RAY DIFFRACTION	r_angle_other_deg	1.015	3	8790
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.402	5	738
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.028	24.306	216
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.231	15	886
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.095	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	875
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6249
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1036
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1164
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	3715
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2655
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	2936
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	164
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.026	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.227	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.285	0.2	55
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.078	1.5	4442
X-RAY DIFFRACTION	r_mcbond_other	0.185	1.5	1550
X-RAY DIFFRACTION	r_mcangle_it	1.398	2	5772
X-RAY DIFFRACTION	r_scbond_it	2.206	3	1984
X-RAY DIFFRACTION	r_scangle_it	3.273	4.5	1657

LS refinement shell

Resolution: 2.23→2.28 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	139	-
R_work	0.275	2480	-
all	-	2619	-
obs	-	2619	96.22 %

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	2.8884	-1.296	-0.7337	1.0178	-0.2451	5.7388	0.0281	-0.2369	0.0826	0.2552	-0.0336	-0.1642	-0.1255	0.2128	0.0055	-0.088	0.0174	-0.0343	-0.024	0.0002	-0.0333	36.7018	43.579	19.9895
2	6.0345	-0.1872	-2.6138	2.8006	-2.9105	8.5345	-0.0939	-0.0413	0.0398	-1.4643	-0.5454	-0.4422	1.3515	1.2267	0.6393	0.5005	0.3294	0.0065	0.0439	0.0356	-0.0857	34.9673	26.6521	37.9123
3	7.7692	1.4373	-2.654	1.8397	-1.1436	1.1772	0.3315	-0.307	-0.3242	0.2111	-0.456	-0.0821	0.467	0.7187	0.1245	0.3524	0.125	-0.0852	0.1197	0.0521	0.0476	31.9716	26.4911	49.7198
4	4.1395	-1.7752	0.1864	3.4872	-2.5349	6.1437	0.2896	-0.5657	-0.3083	0.4085	-0.3852	0.2825	-0.1587	0.3003	0.0956	0.1934	-0.0304	-0.0108	-0.0205	0.027	-0.218	27.1384	34.1175	58.7695
5	1.8544	0.1603	-2.654	0.0138	-0.2294	3.7985	0.0961	-0.3784	-0.0787	-0.0256	-0.4144	-0.0058	0.529	0.8071	0.3183	0.1591	-0.0154	-0.0753	0.2823	0.123	-0.0244	38.4325	43.5517	42.9923
6	11.7911	6.35	5.1064	10.5137	3.9116	4.6097	0.3589	-0.8404	0.4816	1.1867	-0.4333	1.1801	-0.1107	-0.8602	0.0744	0.1222	0.0698	0.0889	0.0524	-0.0294	0.0575	29.3514	51.2722	27.9946
7	4.7824	7.5003	-1.2573	14.1754	-1.915	0.3319	0.0441	0.2812	0.0478	-0.5915	-0.0836	0.0817	-0.0771	-0.2336	0.0396	-0.1607	0.0322	-0.079	0.0175	0.022	0.0705	24.7102	41.3323	17.3324
8	11.9491	-3.6131	4.1967	2.3444	1.9946	9.9817	-0.2235	0.6282	0.9866	0.1149	0.4531	-0.3356	-0.748	0.3568	-0.2296	-0.047	0.0405	0.0072	0.0551	-0.006	0.0548	35.8311	58.953	10.1338
9	1.3489	-1.744	1.695	3.1307	-0.5303	5.2805	-0.2621	0.0063	0.2101	0.1532	0.153	-0.2739	-0.5062	0.2443	0.109	-0.0154	0.047	0.0044	-0.045	0.0216	-0.0016	18.205	65.8506	8.1727
10	4.8037	1.581	1.4192	3.4835	0.3956	0.421	0.3377	0.5202	-0.5075	-0.0901	-0.0905	0.0325	0.3598	0.0296	-0.2472	-0.0522	0.0621	-0.0189	0.0527	0.0008	-0.0521	-4.8665	62.0385	-13.2006
11	3.6591	-1.2559	0.5974	3.9418	-2.1084	1.5669	0.1846	0.682	-0.7344	-0.2492	0.0654	0.0711	0.297	-0.2428	-0.25	-0.0791	0.0301	-0.0321	0.1179	-0.1488	-0.1173	0.1125	54.3014	-21.9173
12	1.5081	2.9158	-1.9533	9.6793	-4.1146	2.5581	-0.3721	0.438	-0.2948	0.2324	0.4723	-0.4587	0.453	-1.6048	-0.1002	-0.0942	-0.1903	-0.0015	0.4305	-0.2987	0.1073	-0.6776	49.1061	-26.2495
13	1.0888	-0.1939	-1.0969	0.1289	-0.0079	1.5429	0.1482	0.0062	-0.1201	0.0388	-0.2142	-0.1389	0.0957	0.0681	0.066	-0.1185	0.0348	-0.0367	-0.0924	0.0259	-0.0356	17.8784	63.6025	-7.8282
14	9.5147	13.8746	-3.9536	28.6251	-8.205	2.3521	-0.5987	0.8076	-0.4889	-1.4507	0.8274	0.2314	0.0368	-0.0922	-0.2288	0.0437	-0.1002	-0.0343	0.0338	-0.0771	-0.0416	11.9945	48.5056	0.1443
15	3.6258	3.8262	-0.2578	4.0691	-0.4123	0.6417	0.0287	-0.1059	-0.4699	-0.1494	0.0755	-0.2776	0.0361	0.3728	-0.1041	-0.1271	0.0236	0.0285	-0.0416	0.006	0.0356	24.5359	57.378	0.5832
16	14.7357	1.1034	1.2796	2.5639	-1.5758	1.4537	0.0651	-0.6677	0.3559	0.2218	0.356	0.386	0.1721	-0.3336	-0.4211	0.0086	0.0188	-0.0118	-0.0256	0.1212	0.0011	18.9368	57.1962	14.4655

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 42	3 - 45
2	X-RAY DIFFRACTION	2	A	A	43 - 80	46 - 83
3	X-RAY DIFFRACTION	3	A	A	81 - 160	84 - 163
4	X-RAY DIFFRACTION	4	A	A	161 - 249	164 - 252
5	X-RAY DIFFRACTION	5	A	A	250 - 286	253 - 289
6	X-RAY DIFFRACTION	6	A	A	287 - 336	290 - 339
7	X-RAY DIFFRACTION	7	A	A	337 - 367	340 - 370
8	X-RAY DIFFRACTION	8	A	A	368 - 380	371 - 383
9	X-RAY DIFFRACTION	9	B	B	-1 - 45	2 - 48
10	X-RAY DIFFRACTION	10	B	B	46 - 165	49 - 168
11	X-RAY DIFFRACTION	11	B	B	166 - 213	169 - 216
12	X-RAY DIFFRACTION	12	B	B	214 - 259	217 - 262
13	X-RAY DIFFRACTION	13	B	B	260 - 293	263 - 296
14	X-RAY DIFFRACTION	14	B	B	294 - 304	297 - 307
15	X-RAY DIFFRACTION	15	B	B	305 - 328	308 - 331
16	X-RAY DIFFRACTION	16	B	B	336 - 379	339 - 382

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