PDB-7la1: Crystal structure of phosphoglycerate kinase from Mycobacterium avium

ID or keywords:

Entry

Database: PDB / ID: 7la1

Title

Crystal structure of phosphoglycerate kinase from Mycobacterium avium

Components

Phosphoglycerate kinase

Keywords

TRANSFERASE / SSGCID /

phosphoglycerate kinase / dimer /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

phosphoglycerate kinase /

phosphoglycerate kinase activity / glycolytic process /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium avium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of phosphoglycerate kinase from Mycobacterium avium
Authors: Bolejack, M.J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jan 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7la1.cif.gz	646 KB	Display	PDBx/mmCIF format
PDB format	pdb7la1.ent.gz	532.8 KB	Display	PDB format
PDBx/mmJSON format	7la1.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/la/7la1 ftp://data.pdbj.org/pub/pdb/validation_reports/la/7la1	HTTPS FTP

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Related structure data

Related structure data	1vpeS S: Starting model for refinement
Similar structure data	1w9z-d 3aza-3 3se5-d 3aza-1 3az9-1 3cf8-d 3azb-4 3az9-4 2glv-2 2glp-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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (7)

Deposited unit

A: Phosphoglycerate kinase

B: Phosphoglycerate kinase

C: Phosphoglycerate kinase

D: Phosphoglycerate kinase

hetero molecules

175 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoglycerate kinase

B: Phosphoglycerate kinase

hetero molecules

defined by author&software
Evidence: gel filtration
87.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphoglycerate kinase

D: Phosphoglycerate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.840, 111.170, 99.270
Angle α, β, γ (deg.)	90.000, 101.870, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphoglycerate kinase / Mass: 43462.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria) Strain: 104 / Gene: pgk, MAV_3340 / Plasmid: MyavA.01331.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QHY4, phosphoglycerate kinase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1887 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.13 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MyavA.01331.a.AE1.PW38721 at 8.6 mg/ml was mixed 1:1 with 25% (w/v) PEG3350 and 100 mM Bis-Tris/HCl pH 5.5 (JCSG+ H3). Stored at 14C. Cryo: 15% EG. Tray 313861h3: puck vml2-8.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 27, 2020 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.6→44.9 Å / Num. obs: 216586 / % possible obs: 99.7 % / Redundancy: 3.891 % / B_iso Wilson estimate: 21.51 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.064 / Χ²: 1.032 / Net I/σ(I): 12.9 / Num. measured all: 842708 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.6-1.64	3.882	0.606	2.06	61979	16011	15965	0.774	0.703	99.7
1.64-1.69	3.887	0.486	2.59	60702	15651	15617	0.847	0.563	99.8
1.69-1.74	3.893	0.374	3.37	59168	15233	15199	0.902	0.434	99.8
1.74-1.79	3.903	0.291	4.33	57306	14719	14682	0.937	0.337	99.7
1.79-1.85	3.902	0.225	5.5	55812	14334	14304	0.961	0.261	99.8
1.85-1.91	3.904	0.167	7.36	53971	13855	13824	0.977	0.194	99.8
1.91-1.98	3.911	0.131	9.26	52018	13346	13301	0.984	0.152	99.7
1.98-2.07	3.914	0.104	11.4	50015	12844	12778	0.989	0.121	99.5
2.07-2.16	3.915	0.086	13.67	48054	12347	12273	0.991	0.1	99.4
2.16-2.26	3.9	0.075	15.81	45902	11805	11770	0.993	0.086	99.7
2.26-2.39	3.903	0.065	17.86	43535	11198	11155	0.994	0.076	99.6
2.39-2.53	3.9	0.058	19.56	41363	10642	10605	0.995	0.068	99.7
2.53-2.7	3.891	0.054	21.34	38750	9990	9959	0.995	0.062	99.7
2.7-2.92	3.881	0.049	23.24	36065	9318	9292	0.995	0.057	99.7
2.92-3.2	3.874	0.046	24.92	33056	8557	8533	0.996	0.053	99.7
3.2-3.58	3.851	0.042	26.62	29773	7758	7732	0.996	0.049	99.7
3.58-4.13	3.861	0.04	27.68	26450	6880	6851	0.997	0.046	99.6
4.13-5.06	3.879	0.038	28.39	22355	5782	5763	0.997	0.044	99.7
5.06-7.16	3.865	0.037	28.19	17481	4535	4523	0.997	0.043	99.7
7.16-44.9	3.639	0.037	28.02	8953	2507	2460	0.996	0.043	98.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19rc4-4035	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1vpe

1vpe

Resolution: 1.6→44.9 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1935	2069	0.96 %
R_work	0.164	214502	-
obs	0.1643	216571	99.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 84.31 Å² / B_iso mean: 28.3993 Å² / B_iso min: 11.25 Å²

Refinement step

Cycle: final / Resolution: 1.6→44.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11833	0	64	1933	13830
B_iso mean	-	-	37.13	36.85	-
Num. residues	-	-	-	-	1644

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.64	0.3334	146	0.2779	14266	14412	100
1.64-1.68	0.2501	131	0.2465	14271	14402	100
1.68-1.72	0.2626	150	0.22	14230	14380	100
1.72-1.77	0.2437	103	0.1976	14331	14434	100
1.77-1.83	0.2261	134	0.1943	14236	14370	100
1.83-1.9	0.2183	162	0.1876	14262	14424	100
1.9-1.97	0.2341	119	0.1919	14277	14396	100
1.97-2.06	0.1843	128	0.1683	14329	14457	100
2.06-2.17	0.1974	153	0.1658	14215	14368	99
2.17-2.31	0.2099	134	0.1634	14301	14435	100
2.31-2.49	0.1901	151	0.1639	14260	14411	100
2.49-2.74	0.2108	149	0.1688	14299	14448	100
2.74-3.13	0.1848	137	0.1621	14351	14488	100
3.13-3.95	0.1696	140	0.1445	14371	14511	100
3.95-44.9	0.1632	132	0.1412	14503	14635	99

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	1.2476	0.0386	0.3376	1.1895	0.027	1.493	0.0189	0.0775	-0.0671	-0.0601	0.0237	-0.1164	0.1412	0.1123	-0.0342	0.116	0.0208	0.0296	0.1155	-0.0152	0.1183	39.6215	-10.8449	11.6692
2	2.2067	-0.1026	1.5968	1.5281	0.4095	2.5902	-0.2986	-0.1146	0.2818	0.0312	-0.0245	0.0817	-0.3498	-0.1235	0.2574	0.2409	0.0093	-0.0562	0.0972	0.0246	0.1997	20.4941	18.835	2.6394
3	1.4799	-1.1769	2.7225	1.9647	-2.563	7.3658	0.063	0.1676	0.0523	-0.1273	0.046	0.0219	0.1962	0.0662	-0.1497	0.1052	-0.0383	-0.0085	0.1259	0.0083	0.1529	37.334	5.2149	10.7735
4	2.0681	-0.0113	-0.1863	1.9332	-0.5871	1.3042	0.0518	-0.0154	0.1964	0.1488	-0.014	0.041	-0.0551	-0.0254	-0.0453	0.1294	-0.0186	0.0264	0.079	-0.004	0.1224	4.8423	-4.7062	5.9658
5	1.177	-0.0317	0.0704	1.3847	-0.5615	1.5101	0.0453	0.0699	-0.0174	-0.0335	0.0179	0.0999	0.1592	-0.0464	-0.0523	0.1397	-0.0326	0.0013	0.1216	0.0034	0.1244	1.9205	-14.7117	0.8711
6	2.3338	-1.6526	-1.2444	2.6353	0.7643	1.4518	-0.0179	-0.2482	0.4279	0.2675	0.2096	-0.5605	-0.1108	0.2803	-0.1551	0.2405	0.011	-0.0606	0.233	-0.0515	0.238	30.5901	-12.9475	-22.1828
7	1.3683	-0.4092	-1.1463	1.7912	-0.4054	1.378	-0.0988	-0.0326	-0.0205	-0.109	0.0213	-0.1705	0.0862	0.1101	0.0452	0.2751	-0.0007	-0.0457	0.2124	-0.011	0.1323	9.4735	-13.1568	-11.6433
8	2.9963	-0.6157	-0.0712	2.2257	0.3389	1.9626	-0.072	0.2477	-0.1612	-0.0764	-0.0021	0.1828	0.0298	-0.3147	0.0308	0.0844	-0.0182	-0.0013	0.1973	0.0172	0.1101	17.7478	-47.2146	53.4128
9	1.0985	0.0597	0.0033	1.1747	0.2561	2.0647	0.0099	0.0546	0.095	-0.0116	-0.0242	0.0385	-0.1846	-0.1924	0.0062	0.0888	0.0182	-0.0041	0.1505	0.0224	0.115	17.2697	-39.4407	57.7964
10	1.6599	-0.5737	0.5315	2.0166	-0.4178	1.3557	-0.0193	-0.131	-0.1544	0.1578	0.0567	0.1714	-0.0086	0.1147	-0.0196	0.1536	-0.0137	0.0217	0.1685	0.0356	0.1116	1.9353	-36.3476	24.255
11	3.5747	2.2895	3.8407	2.8874	2.7693	4.1259	-0.1459	-0.0055	0.0276	-0.3051	-0.0021	0.0734	-0.304	-0.0487	0.1666	0.1804	0.0011	0.0446	0.2642	0.0863	0.1727	18.4087	-38.2089	40.4824
12	5.7062	0.7868	0.8953	2.0568	0.3301	2.3443	-0.1394	-0.0343	0.1888	0.0057	0.0264	-0.2342	-0.031	0.2605	0.0781	0.1417	0.0334	-0.0071	0.2111	0.0027	0.2643	-18.6227	-42.6353	49.3896
13	2.2564	-0.0017	0.0479	2.4755	0.2484	1.1526	-0.1341	-0.2447	0.0142	0.2345	0.1331	-0.1255	0.0475	0.0664	-0.0074	0.1475	0.0332	-0.0008	0.2748	-0.014	0.2355	-22.8695	-45.1809	58.1109
14	6.1961	-0.1258	0.4755	7.4391	1.4387	4.301	-0.2451	-0.5029	-0.048	0.3159	0.0823	0.3098	-0.0576	-0.1647	0.1499	0.1903	0.0216	0.0198	0.2675	0.0502	0.2378	-4.5762	-70.8692	54.424
15	2.9895	0.4157	0.4962	1.1416	0.1793	1.2664	-0.0514	-0.0598	-0.0037	0.0114	0.0202	-0.1198	-0.0602	0.0237	0.0335	0.1756	-0.0091	-0.0027	0.1893	-0.0114	0.2111	6.0346	-69.2318	48.4243
16	6.5385	-3.5729	0.3558	9.2906	-0.2587	8.063	-0.3776	-0.6199	-0.5924	0.4918	0.5036	-0.4586	0.2851	0.5983	-0.0816	0.2624	0.0354	-0.0178	0.2765	-0.0009	0.2972	-18.5575	-60.1028	60.4052

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 through 196 )	A	0 - 196
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 197 through 373 )	A	197 - 373
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 374 through 411 )	A	374 - 411
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 112 )	B	1 - 112
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 113 through 195 )	B	113 - 195
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 196 through 373 )	B	196 - 373
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 374 through 411 )	B	374 - 411
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 0 through 56 )	C	0 - 56
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 57 through 196 )	C	57 - 196
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 197 through 373 )	C	197 - 373
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 374 through 411 )	C	374 - 411
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 2 through 91 )	D	2 - 91
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 92 through 196 )	D	92 - 196
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 197 through 224 )	D	197 - 224
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 225 through 386 )	D	225 - 386
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 387 through 410 )	D	387 - 410

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