PDB-5um0: Crystal structure of 2,3-bisphosphoglycerate-dependent phosphogly...

ID or keywords:

Entry

Database: PDB / ID: 5um0

Title

Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from Neisseria gonorrhoeae

Components

2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

Keywords

ISOMERASE / SSGCID / 2 / 3-bisphosphoglycerate-dependent phosphoglycerate mutase / mutase / pyruvate synthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process
Similarity search - Function

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from Neisseria gonorrhoeae
Authors: Abendroth, J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Jan 25, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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	5um0.cif.gz	402.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5um0.ent.gz	329.1 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/5um0 ftp://data.pdbj.org/pub/pdb/validation_reports/um/5um0	HTTPS FTP

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Related structure data

Related structure data	3gp3S S: Starting model for refinement
Similar structure data	1rii-d 4odi-d 3kkk-d 4pgm-d 1bq4-d 5pgm-2 3sjb-d 1zxn-1 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: SSGCID-NegoA.01013.a TargetTrack: NegoA.01013.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#257 - May 2021 Fetal Hemoglobin similarity (6) #50 - Feb 2004 Glycolytic Enzymes similarity (6) #225 - Sep 2018 Phytase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

C: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

D: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	71.580, 73.030, 96.930
Angle α, β, γ (deg.)	90.000, 97.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / dPGM Mass: 26997.771 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria) Strain: NCCP11945 / Gene: gpmA, NGK_0248 / Plasmid: NegoA.01013.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B4RIY7, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 948 / 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: 2.33 Å³/Da / Density % sol: 47.2 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Microlytics MCSG1 screen, condition: E10: 20% ammonium tartrate, 20% PEG 3350: NegoA.01013.a.B1.PS38022 at 14.0mg/ml: cryo: 20% EG: tray: 284241 e10: puck: qsy1-3.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 30, 2016

Radiation

Monochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.85→42.5 Å / Num. obs: 84511 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.116 % / B_iso Wilson estimate: 24.52 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.065 / R_rim(I) all: 0.071 / Χ²: 1.09 / Net I/σ(I): 14.12

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	3.074	0.356	2.45	6213	6213	0.87	0.435	99.4
1.9-1.95	3.196	0.277	3.27		6031	0.913	0.335	99.8
1.95-2.01	3.297	0.225	4.04		5889	0.943	0.27	99.5
2.01-2.07	3.421	0.181	5.26		5721	0.961	0.216	99.5
2.07-2.14	3.718	0.153	6.79		5572	0.975	0.179	99.8
2.14-2.21	4.467	0.136	8.92		5374	0.983	0.154	100
2.21-2.29	4.823	0.111	11.39		5174	0.989	0.125	99.9
2.29-2.39	5.03	0.102	12.5		5012	0.992	0.114	99.9
2.39-2.49	5.276	0.097	13.72		4813	0.993	0.107	99.9
2.49-2.62	5.626	0.09	14.9		4584	0.994	0.1	100
2.62-2.76	6.145	0.083	17.53		4364	0.995	0.091	99.8
2.76-2.93	7.146	0.079	20.5		4148	0.996	0.086	99.8
2.93-3.13	7.236	0.073	22.75		3889	0.996	0.079	100
3.13-3.38	7.185	0.067	25.35		3604	0.997	0.072	99.9
3.38-3.7	7.049	0.059	27.98		3340	0.997	0.064	99.9
3.7-4.14	6.902	0.054	29.77		3032	0.997	0.059	99.9
4.14-4.78	6.913	0.051	30.67		2700	0.998	0.055	100
4.78-5.85	6.989	0.05	30.28		2264	0.997	0.054	99.9
5.85-8.27	7.062	0.049	30.14		1782	0.998	0.053	99.9
8.27-42.471	6.854	0.044	32.33		1005	0.997	0.047	98.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2 Å	43.3 Å
Translation	2 Å	43.3 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building
PHENIX	dev_2650	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3gp3-A

3gp3

Resolution: 1.85→42.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.07

	R_factor	Num. reflection	% reflection
R_free	0.2086	2071	2.45 %
R_work	0.1659	-	-
obs	0.1669	84479	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 109.82 Å² / B_iso mean: 33.4262 Å² / B_iso min: 11.22 Å²

Refinement step

Cycle: final / Resolution: 1.85→42.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7280	0	50	958	8288
B_iso mean	-	-	51.87	40.23	-
Num. residues	-	-	-	-	918

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7614
X-RAY DIFFRACTION	f_angle_d	0.774	10357
X-RAY DIFFRACTION	f_chiral_restr	0.051	1146
X-RAY DIFFRACTION	f_plane_restr	0.005	1350
X-RAY DIFFRACTION	f_dihedral_angle_d	13.87	4590

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 (%)
1.85-1.8931	0.2806	146	0.2284	5448	5594	99
1.8931-1.9404	0.2796	140	0.2156	5462	5602	100
1.9404-1.9929	0.2709	132	0.1999	5458	5590	100
1.9929-2.0515	0.2655	130	0.1921	5431	5561	100
2.0515-2.1177	0.2054	131	0.1877	5454	5585	100
2.1177-2.1934	0.238	164	0.1855	5467	5631	100
2.1934-2.2812	0.2151	143	0.1738	5498	5641	100
2.2812-2.3851	0.233	139	0.1734	5472	5611	100
2.3851-2.5108	0.2288	138	0.1776	5482	5620	100
2.5108-2.6681	0.2636	136	0.1862	5498	5634	100
2.6681-2.874	0.2315	139	0.1788	5500	5639	100
2.874-3.1632	0.2175	138	0.1728	5491	5629	100
3.1632-3.6207	0.2035	120	0.1573	5551	5671	100
3.6207-4.5608	0.165	146	0.13	5535	5681	100
4.5608-42.4824	0.1606	129	0.1492	5661	5790	100

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	1.8139	-1.0578	0.3103	6.6007	-1.1157	2.4084	0.0156	0.2019	0.088	-0.2861	0.0748	0.249	-0.007	-0.2372	-0.0679	0.1146	0.0024	0.0133	0.2052	0.0185	0.1893	19.2419	-6.4009	103.3218
2	1.3403	0.9556	-0.2524	4.1361	-1.389	3.8201	-0.0273	0.1566	-0.1439	-0.3286	0.0676	0.0969	0.4336	-0.1069	-0.06	0.1194	-0.0043	0.0107	0.1867	-0.0196	0.1512	23.1002	-13.4935	100.9042
3	1.5196	0.3211	-0.151	1.7604	-0.6682	1.9538	-0.0278	0.0218	-0.0531	-0.0552	0.0826	0.0132	0.1344	-0.1224	-0.0381	0.1057	0.0073	0.0018	0.1161	-0.0143	0.123	26.2221	-7.0628	107.0084
4	6.1071	-1.5484	-1.3472	5.3869	1.3383	7.138	0.0014	-0.1981	-0.4757	0.0885	0.0655	0.3949	0.2749	-0.2801	-0.0332	0.3218	-0.1195	-0.047	0.2261	0.0713	0.3076	8.9313	-27.0212	114.5926
5	5.0342	0.3456	-0.2737	2.7925	-0.4376	1.1736	-0.0461	-0.4102	-0.1961	0.2558	-0.0569	-0.1867	0.1805	-0.0251	0.0891	0.3293	-0.0108	-0.0213	0.29	0.0613	0.2177	25.2151	-17.4338	122.5948
6	1.7106	0.4064	-0.2854	2.2547	-0.1349	2.2362	0.0115	-0.1934	0.0936	0.122	-0.0137	0.1753	0.0736	-0.2075	-0.001	0.122	0.0207	0.0079	0.1799	-0.0103	0.1767	16.3498	-2.0269	113.5947
7	4.0861	-0.0723	0.3791	8.0719	3.3338	7.2119	0.0884	0.1507	0.3706	-0.1018	-0.1873	0.3821	-0.4107	-0.6188	0.1307	0.1331	0.0519	0.0059	0.2183	0.0589	0.2488	11.8807	6.6382	105.9861
8	3.145	-0.1887	0.8658	3.5033	-0.0269	5.0775	0.2314	0.1016	-0.3607	-0.3497	0.0504	-0.2608	0.5879	0.3944	-0.2358	0.1232	0.0167	0.0537	0.1258	-0.0535	0.3175	49.5351	-6.9978	97.0859
9	1.4507	0.3992	0.1561	2.3901	-0.2831	1.7909	-0.0542	0.0848	-0.2465	-0.1503	0.039	-0.1215	0.1274	0.0784	0.0164	0.1052	0.0099	0.0229	0.1107	-0.0342	0.1661	43.9691	-4.3453	98.2514
10	3.1581	1.4074	-0.4215	6.942	0.5959	0.1542	0.0698	0.8222	0.2139	-0.5023	0.3433	-1.0359	0.1479	0.1916	-0.4323	0.5411	-0.1753	0.2298	0.58	-0.1433	0.5028	59.2761	8.6256	80.3719
11	1.3285	0.0225	0.6206	1.5991	-0.4876	2.1693	-0.0942	0.0845	0.0418	-0.0939	0.0374	-0.2991	-0.092	0.2211	0.0591	0.1255	-0.0166	0.0271	0.1381	-0.0357	0.19	51.7993	6.0142	100.5855
12	5.9169	-0.681	1.6394	7.7943	2.07	6.7663	0.0176	-0.0541	-0.5019	0.3933	0.3815	-0.8287	0.5166	0.6124	-0.3558	0.1795	0.0723	-0.0077	0.2053	-0.0069	0.3456	59.5039	-9.6456	110.6411
13	2.9295	0.1622	0.2838	4.9902	0.3121	5.8611	0.0558	-0.7604	0.6775	-0.0516	0.1227	-0.1531	-0.5764	-0.1934	-0.1253	0.327	0.036	0.0651	0.3034	-0.1132	0.2442	46.9343	29.0869	124.9908
14	2.0394	0.0121	-0.4753	1.3354	0.2235	1.4747	0.0486	-0.5031	0.4473	0.1932	-0.023	-0.011	-0.3111	0.0047	-0.0079	0.2662	0.009	-0.0145	0.262	-0.0858	0.2076	46.9292	23.8094	127.7069
15	5.1623	1.4512	0.0647	1.3567	0.9114	2.7522	-0.0893	-0.3386	0.1161	-0.0003	-0.0118	-0.2809	-0.3074	0.3863	0.137	0.2201	0.0069	-0.0409	0.3115	-0.0192	0.2282	67.2663	21.0495	124.0911
16	4.8715	1.6884	0.7428	8.3769	-2.0153	4.6646	0.0782	0.2502	-0.408	-0.1884	0.0671	0.3469	0.3116	-0.0694	-0.1422	0.2111	-0.0132	-0.059	0.2185	-0.0111	0.3173	58.4303	9.5797	119.9632
17	3.7803	0.5114	-0.5779	1.777	-0.0023	2.4725	0.0631	-0.0314	0.2902	-0.0213	-0.0572	0.0617	-0.4942	-0.0217	0.0066	0.2722	0.0079	-0.0238	0.1398	-0.0212	0.1612	49.0038	24.7717	113.644
18	4.2221	-1.2592	-0.8612	3.2579	-2.9504	5.3025	0.4373	0.1952	0.2685	-0.7064	-0.3764	0.4718	-1.0418	-0.3584	-0.0896	0.5031	0.1154	-0.1003	0.2076	0.014	0.4656	39.8306	32.8637	110.6498
19	3.6143	-0.8222	-1.5969	1.0501	1.6737	2.9823	-0.3352	-1.0179	0.2467	0.4597	0.4252	-0.0969	0.0008	0.3665	-0.0871	0.3119	-0.0356	-0.0129	0.4824	-0.0097	0.2171	32.3816	9.5974	142.9207
20	3.4265	1.8675	-1.5408	2.8332	-1.0011	0.7159	0.0421	-0.8965	0.2099	0.4429	-0.1511	-0.0928	-0.4834	-0.155	0.1108	0.3298	0.0382	0.0054	0.4682	-0.1167	0.2817	23.0288	19.5005	141.5933
21	7.3716	-1.5734	-0.3742	6.2479	1.1013	3.3615	-0.0327	-1.1063	0.1727	0.7609	-0.3182	-0.0168	-0.2036	0.1562	0.3179	0.3677	-0.1004	-0.0714	0.7803	-0.0357	0.272	41.66	13.9279	146.8607
22	1.1659	0.1758	-0.2891	1.7208	0.0294	1.4555	0.0284	-0.5585	0.0856	0.1573	-0.0888	-0.0313	-0.2063	0.0555	0.0719	0.2276	-0.0073	-0.0122	0.364	-0.0256	0.1558	33.3092	11.4448	136.0359
23	3.4125	2.3886	-0.3712	8.3878	1.0429	2.3515	0.3664	-0.3589	0.5801	0.9436	-0.3676	0.5916	-0.0904	-0.6716	0.0049	0.5605	-0.0179	0.1201	0.7673	-0.0949	0.6012	9.1078	12.2558	149.9044
24	4.2365	0.261	-1.0489	3.9268	-0.4037	2.0805	0.0996	-0.4393	0.4412	0.0734	-0.1483	0.5424	-0.1372	-0.3347	-0.0013	0.2314	0.0559	-0.0495	0.4298	-0.1281	0.3206	14.4964	14.6148	132.4477
25	3.0757	0.9208	-2.5427	4.8486	-3.7263	9.1861	-0.0012	-0.2329	-0.3247	-0.1217	-0.2966	0.1167	0.1817	-0.0203	0.263	0.249	0.0584	-0.0141	0.34	-0.0654	0.2632	17.2199	10.1856	126.9077
26	4.0877	-0.5136	0.3451	2.7029	0.0684	2.6684	0.0545	-0.2852	-0.3459	0.0604	-0.0492	0.0889	0.0345	-0.0345	-0.0234	0.199	0.0028	-0.0041	0.2725	0.0285	0.1772	30.6546	0.0851	131.6298
27	2.5275	0.6397	-0.572	3.9788	-0.1833	1.3997	0.2768	-0.8467	-0.2252	0.8428	-0.1612	0.0469	-0.0214	-0.0417	-0.1066	0.3971	-0.0732	0.0059	0.5742	0.085	0.2648	26.2856	-0.8136	144.2411
28	5.6605	1.1674	3.6382	5.2207	2.3146	2.9516	0.4637	-0.9906	-0.967	0.7277	-0.2118	-0.4492	0.7492	0.5148	-0.3318	0.4222	-0.0308	-0.0734	0.7237	0.2682	0.4631	38.0711	-6.7487	142.1064

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 -2 through 16 )	A	-2 - 16
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 44 )	A	17 - 44
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 96 )	A	45 - 96
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 97 through 113 )	A	97 - 113
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 114 through 150 )	A	114 - 150
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 151 through 210 )	A	151 - 210
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 211 through 227 )	A	211 - 227
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -2 through 17 )	B	-2 - 17
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 18 through 96 )	B	18 - 96
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 97 through 114 )	B	97 - 114
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 115 through 210 )	B	115 - 210
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 211 through 227 )	B	211 - 227
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -2 through 16 )	C	-2 - 16
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 17 through 96 )	C	17 - 96
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 97 through 137 )	C	97 - 137
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 138 through 150 )	C	138 - 150
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 151 through 210 )	C	151 - 210
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 211 through 227 )	C	211 - 227
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 0 through 15 )	D	0 - 15
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 16 through 28 )	D	16 - 28
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 29 through 44 )	D	29 - 44
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 45 through 96 )	D	45 - 96
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 97 through 114 )	D	97 - 114
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 115 through 137 )	D	115 - 137
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 138 through 150 )	D	138 - 150
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 151 through 181 )	D	151 - 181
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 182 through 210 )	D	182 - 210
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 211 through 227 )	D	211 - 227

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