PDB-4ehj: An X-ray Structure of a Putative Phosphogylcerate Kinase from Fra...

ID or keywords:

Entry

Database: PDB / ID: 4ehj

Title

An X-ray Structure of a Putative Phosphogylcerate Kinase from Francisella tularensis subsp. tularensis SCHU S4

Components

Phosphoglycerate kinase

Keywords

TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / ATP binding / cytosol
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.71 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: An X-ray Structure of a Putative Phosphogylcerate Kinase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Apr 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 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_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_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	4ehj.cif.gz	310.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ehj.ent.gz	256.7 KB	Display	PDB format
PDBx/mmJSON format	4ehj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ehj_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	4ehj_full_validation.pdf.gz	442.2 KB	Display
Data in XML	4ehj_validation.xml.gz	34.4 KB	Display
Data in CIF	4ehj_validation.cif.gz	46.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eh/4ehj ftp://data.pdbj.org/pub/pdb/validation_reports/eh/4ehj	HTTPS FTP

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Related structure data

Similar structure data	4fey-d 5bt8-4 6i06-d 4dg5-d 4cn8-d 6hxe-d 4q2k-1 3s0z-d 1eps-d 5tic-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) 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	TargetTrack: IDP02760

Similar structure data

Other databases

TargetTrack: IDP02760

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (7)

Deposited unit

A: Phosphoglycerate kinase

B: Phosphoglycerate kinase

hetero molecules

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

1

A: Phosphoglycerate kinase

hetero molecules

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

2

B: Phosphoglycerate kinase

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

3

A: Phosphoglycerate kinase

hetero molecules

B: Phosphoglycerate kinase

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

Unit cell

Length a, b, c (Å)	98.733, 117.185, 143.759
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-423- HOH

#1: Protein	Phosphoglycerate kinase Mass: 42266.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4/Schu 4 / Gene: FTT_1367c, pgk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5NF76, phosphoglycerate kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.46 Å³/Da / Density % sol: 49.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3350 25%, MgCl2 0.2M, Tris 0.1M pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2009 / Details: Be Lenses
Radiation	Monochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2.7→30 Å / Num. all: 22986 / Num. obs: 22986 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / B_iso Wilson estimate: 57.73 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 51.96
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 14.4 % / R_merge(I) obs: 0.513 / Mean I/σ(I) obs: 6.16 / Num. unique all: 1129 / % possible all: 100

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Processing

Software

Name	Version	Classification
BLU-MAX		data collection
PHENIX		model building
BUSTER	2.10.0	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.71→29.66 Å / Cor.coef. F_o:F_c: 0.9462 / Cor.coef. F_o:F_c free: 0.9213 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2177	1179	5.14 %	RANDOM
R_work	0.1679	-	-	-
obs	0.1705	22950	99.82 %	-
all	-	22950	-	-

Displacement parameters

B_iso mean: 59.18 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1803 Å²	0 Å²	0 Å²
2-	-	3.1486 Å²	0 Å²
3-	-	-	-3.3289 Å²

Refine analyze

Luzzati coordinate error obs: 0.352 Å

Refinement step

Cycle: LAST / Resolution: 2.71→29.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5818	0	5	258	6081

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	5902	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.11	7983	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d	2.91	2780	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes		142	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		846	HARMONIC	5
X-RAY DIFFRACTION	t_it		5902	HARMONIC	20
X-RAY DIFFRACTION	t_omega_torsion	2.65
X-RAY DIFFRACTION	t_other_torsion	2.91
X-RAY DIFFRACTION	t_chiral_improper_torsion		814	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		6865	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.71→2.83 Å / Total num. of bins used: 12

	R_factor	Num. reflection	% reflection
R_free	0.2833	137	5.01 %
R_work	0.1792	2599	-
all	0.1842	2736	-
obs	-	-	99.82 %

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	6.3156	-0.6592	-3.5209	2.8721	-0.4249	7.8308	-0.0522	-0.6235	-0.0952	0.346	0.4	0.5959	0.3048	-0.1655	-0.3479	-0.156	0.0531	0.175	-0.0569	0.1737	-0.1568	69.3519	8.093	53.6388
2	1.1758	-1.4104	-4.4962	6.7953	-4.7603	3.2434	-0.0558	-0.3792	-0.6369	0.1663	0.2335	-0.153	0.0435	0.1243	-0.1777	0.0277	0.1661	0.1417	0.2228	0.2273	-0.2321	75.519	0.19	56.1587
3	5.2438	-0.0672	-0.0762	2.6825	0.1475	4.4462	0.0867	0.0547	-0.3568	0.3746	0.4039	1.1237	0.4964	-1.1173	-0.4907	-0.194	-0.1092	0.2254	0.0196	0.278	0.0251	60.6514	6.4097	50.2355
4	0	-6.1284	0.2959	0	1.5842	0	-0.0377	-0.1191	0.2226	0.1192	0.0178	0.1462	0.0645	-0.2593	0.0199	0.0567	0.2172	0.3817	-0.0702	-0.0473	0.1716	68.1972	32.2587	45.5707
5	2.5441	0.6498	0.9357	0.7991	-1.6377	4.1433	-0.2493	0.5095	0.2206	-0.1377	0.4263	0.4383	-0.2404	-1.0245	-0.177	-0.0853	0.001	-0.0348	0.0602	0.1284	-0.1687	76.1466	32.7857	23.7711
6	0	1.7326	3.8744	4.9627	1.8732	3.5083	-0.0363	0.6007	-0.0164	-0.0009	0.1417	-0.2084	0.407	0.0928	-0.1054	0.0034	-0.1901	0.1603	0.2276	-0.0361	-0.0746	96.5832	25.7654	20.5036
7	4.6655	-0.2134	-0.3414	4.4981	-1.1567	1.7329	-0.3626	0.4331	0.1637	0.1169	0.4596	0.0874	-0.4321	0.0402	-0.097	0.0053	-0.0566	0.0207	0.0311	0.0177	-0.1551	87.7421	32.3054	30.5523
8	6.0886	1.4473	-1.6122	4.1895	-1.8014	2.4128	-0.1505	0.2744	0.1785	0.5583	0.5917	0.7375	-0.2142	-0.616	-0.4412	-0.0364	0.1466	0.1249	-0.0691	0.0396	-0.2056	77.4474	25.1704	41.5583
9	1.4434	-1.788	2.5488	1.4162	-1.0964	0.807	0.0209	0.0775	0.0751	0.1874	-0.0358	0.0389	0.0229	-0.0395	0.0149	-0.095	0.0949	0.3261	0.3038	0.288	0.1631	54.836	19.8481	47.5364
10	7.0358	2.1537	0.9693	5.4974	0.5058	6.6185	-0.0319	0.8219	-1.3422	-0.077	0.4473	-0.8998	0.2482	0.979	-0.4154	-0.2701	-0.0413	-0.0025	-0.1413	-0.1751	0.0667	89.41	73.7807	75.109
11	6.0849	2.296	-0.6195	8.2118	3.0434	6.6242	-0.2225	0.442	-0.3392	0.2836	0.3059	-0.5938	-0.4854	0.57	-0.0834	-0.109	-0.1616	-0.129	-0.0332	-0.0562	-0.0905	89.7526	83.9622	79.9366
12	5.1107	2.921	3.1567	2.5484	1.0438	1.1538	-0.0112	0.092	0.1753	0.1233	0.0461	-0.1023	-0.4502	-0.0276	-0.0349	-0.0245	0.0192	-0.0035	-0.1307	-0.0196	-0.1729	73.3455	77.6202	76.3928
13	4.5398	0.0148	1.5268	4.844	-2.7737	7.2704	0.1662	-0.3594	0.184	0.6229	0.3592	0.2924	-0.9243	-0.9453	-0.5254	-0.1478	0.0883	0.1013	0.0436	0.0285	-0.2754	59.4652	65.342	93.4268
14	0.5646	-1.1624	-2.5353	1.56	-5.0176	4.4213	0.0248	0.0667	0.0058	0.2025	0.1155	0.1918	0.145	-0.4891	-0.1404	0.0252	-0.0176	0.0516	0.4888	0.2107	-0.2177	57.9251	57.362	107.761
15	5.7764	-3.2668	-5.4124	8.1874	-1.2352	4.8205	0.0598	-0.0585	0.5135	0.9373	0.3972	0.476	-0.4184	-0.4101	-0.457	0.0273	0.2755	0.2118	0.3008	0.0906	-0.2153	53.5486	67.5044	99.8288
16	1.8596	-1.0925	1.0959	4.899	-5.2191	11.2604	0.2105	-0.6198	-0.3198	-0.1254	0.2398	0.1336	0.7755	-0.73	-0.4502	-0.1618	-0.1557	-0.0655	0.0561	0.1485	-0.1197	62.332	50.3045	95.7261
17	1.4408	0.3948	-0.5393	4.1479	0.0814	6.7271	0.0691	-0.25	-0.1826	-0.0897	-0.0403	-0.3499	-0.1821	0.0796	-0.0288	-0.1716	-0.0013	0.0015	-0.0689	0.0376	-0.0815	69.4656	58.3724	81.3256
18	1.4573	-0.8921	-4.2017	0.3301	-2.9007	0	0.0067	0.1255	0.0812	0.1667	-0.0314	0.1025	-0.1045	0.0304	0.0247	0.233	0.0313	0.1322	-0.0518	-0.0736	-0.0186	66.4385	76.3321	85.8636
19	1.5337	-3.0591	1.7949	3.8606	-0.2295	0	0.0293	0.1619	0.3546	-0.0208	-0.0773	0.3651	-0.306	-0.37	0.048	0.0977	-0.0184	-0.0568	-0.0029	0.0632	0.0179	71.2857	85.7933	75.95
20	0	-0.0141	-0.0166	0.0033	0.0147	0	-0.0004	0.0033	-0.0001	-0.0014	0.0004	0.002	0.0002	-0.0024	0	0.0455	0.0845	0.0456	0.057	0.1138	-0.0382	84.8894	20.8284	28.9472

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|2 - A\|70 }	A	2 - 70
2	X-RAY DIFFRACTION	2	{ A\|71 - A\|91 }	A	71 - 91
3	X-RAY DIFFRACTION	3	{ A\|92 - A\|169 }	A	92 - 169
4	X-RAY DIFFRACTION	4	{ A\|170 - A\|183 }	A	170 - 183
5	X-RAY DIFFRACTION	5	{ A\|184 - A\|265 }	A	184 - 265
6	X-RAY DIFFRACTION	6	{ A\|266 - A\|278 }	A	266 - 278
7	X-RAY DIFFRACTION	7	{ A\|279 - A\|336 }	A	279 - 336
8	X-RAY DIFFRACTION	8	{ A\|337 - A\|380 }	A	337 - 380
9	X-RAY DIFFRACTION	9	{ A\|381 - A\|391 }	A	381 - 391
10	X-RAY DIFFRACTION	10	{ B\|2 - B\|101 }	B	2 - 101
11	X-RAY DIFFRACTION	11	{ B\|102 - B\|132 }	B	102 - 132
12	X-RAY DIFFRACTION	12	{ B\|133 - B\|184 }	B	133 - 184
13	X-RAY DIFFRACTION	13	{ B\|185 - B\|222 }	B	185 - 222
14	X-RAY DIFFRACTION	14	{ B\|223 - B\|233 }	B	223 - 233
15	X-RAY DIFFRACTION	15	{ B\|234 - B\|255 }	B	234 - 255
16	X-RAY DIFFRACTION	16	{ B\|256 - B\|334 }	B	256 - 334
17	X-RAY DIFFRACTION	17	{ B\|335 - B\|372 }	B	335 - 372
18	X-RAY DIFFRACTION	18	{ B\|373 - B\|380 }	B	373 - 380
19	X-RAY DIFFRACTION	19	{ B\|381 - B\|391 }	B	381 - 391
20	X-RAY DIFFRACTION	20	{ A\|401 - A\|401 }	A	401

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