PDB-5vve: Crystal structure of phosphoglycerate mutase from Naegleria fowleri

ID or keywords:

Entry

Database: PDB / ID: 5vve

Title

Crystal structure of phosphoglycerate mutase from Naegleria fowleri

Components

Phosphoglycerate mutase

Keywords

ISOMERASE / SSGCID / Structural Genomics / Naegleria fowleri / phosphoglycerate mutase / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

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

Biological species

Naegleria fowleri (brain-eating amoeba)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of phosphoglycerate mutase from Naegleria fowleri
Authors: Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	May 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 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	5vve.cif.gz	232.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5vve.ent.gz	186.1 KB	Display	PDB format
PDBx/mmJSON format	5vve.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vve_validation.pdf.gz	447.1 KB	Display	wwPDB validaton report
Full document	5vve_full_validation.pdf.gz	448.5 KB	Display
Data in XML	5vve_validation.xml.gz	26.2 KB	Display
Data in CIF	5vve_validation.cif.gz	39.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/5vve ftp://data.pdbj.org/pub/pdb/validation_reports/vv/5vve	HTTPS FTP

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Related structure data

Related structure data	1e58S S: Starting model for refinement
Similar structure data	6tbg-8 4ac8-1 1abr-d 6ein-d 5py8-d 2hjr-10 6tbg-7 2pk9-2 5y2o-1 4m1h-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-NafoA.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 (8) #50 - Feb 2004 Glycolytic Enzymes similarity (8) #225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Phosphoglycerate mutase

B: Phosphoglycerate mutase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	77.610, 89.330, 157.880
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	B-686- HOH

#1: Protein	Phosphoglycerate mutase / NafoA.01013.a.B1 Mass: 30004.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Strain: ATCC 30863 / Gene: NF0048460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCG6*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.28 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Micolytic MCSG1 A7: 200mM MgCl2, 25% PEG 3350, 100mM BisTris HCl pH 5.5:NafoA.0013.a.B1.PS38236 at 18.9mg/ml: crystals soaked for 3h with 2.5mM 3-Pospho-glycerate (BSI 1959, not visible in ...Details: Micolytic MCSG1 A7: 200mM MgCl2, 25% PEG 3350, 100mM BisTris HCl pH 5.5:NafoA.0013.a.B1.PS38236 at 18.9mg/ml: crystals soaked for 3h with 2.5mM 3-Pospho-glycerate (BSI 1959, not visible in structure): cryo: 20% EG, tray: 290723a7, puck wvn8-2

Crystal

Density Matthews: 2.28 Å³/Da / Density % sol: 46.2 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Micolytic MCSG1 A7: 200mM MgCl2, 25% PEG 3350, 100mM BisTris HCl pH 5.5:NafoA.0013.a.B1.PS38236 at 18.9mg/ml: crystals soaked for 3h with 2.5mM 3-Pospho-glycerate (BSI 1959, not visible in ...

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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: May 1, 2016 / Details: RIGAKU VARIMAX

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.7→47.046 Å / Num. obs: 60168 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 12.494 % / B_iso Wilson estimate: 19.42 Å² / CC_1/2: 1 / R_merge(I) obs: 0.042 / R_rim(I) all: 0.044 / Χ²: 1.081 / Net I/σ(I): 34.11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	5.942	0.431	3.69	4118	0.947	0.473	93.1
1.74-1.79	7.741	0.361	5.28	4311	0.974	0.387	99.2
1.79-1.84	8.055	0.304	6.44	4200	0.984	0.325	99.7
1.84-1.9	8.419	0.232	8.37	4068	0.991	0.247	99.8
1.9-1.96	8.802	0.185	10.83	3945	0.993	0.196	99.8
1.96-2.03	9.176	0.144	13.91	3837	0.996	0.153	99.9
2.03-2.11	9.736	0.115	17.96	3733	0.997	0.122	99.9
2.11-2.19	11.774	0.094	24.28	3546	0.998	0.099	99.9
2.19-2.29	12.856	0.082	29.77	3433	0.999	0.085	99.7
2.29-2.4	13.508	0.071	34.11	3270	0.999	0.073	99.8
2.4-2.53	14.311	0.061	39.75	3092	0.999	0.063	99.6
2.53-2.69	15.561	0.057	43.71	2970	1	0.059	99.8
2.69-2.87	18.047	0.048	55.32	2792	1	0.05	99.7
2.87-3.1	19.907	0.044	64.04	2592	1	0.045	99.8
3.1-3.4	19.79	0.037	75.69	2414	1	0.038	99.9
3.4-3.8	19.442	0.031	87.7	2180	1	0.032	100
3.8-4.39	19.259	0.028	96.19	1933	1	0.029	99.9
4.39-5.38	19.079	0.026	96.68	1661	1	0.027	99.8
5.38-7.6	19.033	0.027	92.24	1307	1	0.028	100
7.6-47.046	17.106	0.024	99.24	766	1	0.025	99.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MoRDa		phasing
PHENIX		model building
Coot		model building
PHENIX	dev_2776	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1e58, found by Morda

1e58

Resolution: 1.7→47.046 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.55

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1947	2059	3.42 %	RANDOM
R_work	0.1649	-	-	-
obs	0.1659	60142	99.22 %	-

Solvent computation

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

Displacement parameters

B_iso max: 94.59 Å² / B_iso mean: 27.7416 Å² / B_iso min: 9.84 Å²

Refinement step

Cycle: final / Resolution: 1.7→47.046 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3965	0	29	605	4599
B_iso mean	-	-	30.69	37.27	-
Num. residues	-	-	-	-	489

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4233
X-RAY DIFFRACTION	f_angle_d	0.928	5759
X-RAY DIFFRACTION	f_chiral_restr	0.057	627
X-RAY DIFFRACTION	f_plane_restr	0.006	729
X-RAY DIFFRACTION	f_dihedral_angle_d	15.544	2594

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 (%)
1.7-1.7396	0.2909	136	0.2242	3557	3693	92
1.7396-1.7831	0.2635	128	0.2079	3809	3937	99
1.7831-1.8313	0.2331	135	0.203	3859	3994	100
1.8313-1.8852	0.2596	134	0.1955	3847	3981	100
1.8852-1.946	0.2237	140	0.1826	3853	3993	100
1.946-2.0156	0.2029	150	0.1758	3849	3999	100
2.0156-2.0963	0.2207	145	0.1715	3863	4008	100
2.0963-2.1917	0.186	144	0.1697	3869	4013	100
2.1917-2.3072	0.2041	138	0.1744	3863	4001	100
2.3072-2.4518	0.1808	126	0.1733	3900	4026	100
2.4518-2.6411	0.2219	127	0.1809	3887	4014	100
2.6411-2.9068	0.2206	123	0.1716	3934	4057	100
2.9068-3.3273	0.1746	152	0.1636	3896	4048	100
3.3273-4.1917	0.1793	130	0.1353	3983	4113	100
4.1917-47.0638	0.1606	151	0.149	4114	4265	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	2.8117	0.654	-0.1709	5.5916	-0.329	4.0418	-0.0847	-0.1879	0.1537	0.2173	0.0648	-0.2174	-0.2472	0.1542	-0.0296	0.1693	0.0297	-0.0075	0.1532	-0.028	0.1559	21.5434	-5.7172	48.0734
2	2.3267	-0.2776	-0.6656	4.0597	-0.434	4.5441	-0.0297	-0.2995	-0.029	0.1654	0.0538	0.8219	-0.0007	-0.7297	-0.0454	0.2374	0.0219	0.0338	0.2735	-0.0096	0.3547	10.6215	-5.6753	50.5386
3	8.6786	-3.3186	-0.3901	3.9562	0.1306	1.4562	-0.1678	-0.1614	-0.4367	0.0259	0.2011	-0.4799	0.5334	0.4098	0.0115	0.3071	0.1211	0.0119	0.247	-0.0285	0.2775	35.1065	-36.2824	16.4304
4	2.385	-0.2978	0.9072	5.5841	-2.0374	4.4501	-0.0574	0.2993	-0.0723	-0.1722	0.2955	0.7832	-0.0016	-0.4544	-0.2266	0.1808	-0.0025	-0.0396	0.2406	0.0476	0.2408	9.5179	-16.4803	12.3679
5	6.6417	-4.0429	3.0444	3.6467	-4.0525	5.492	0.209	0.1041	-0.3655	-0.1401	0.0634	0.6803	0.4922	-0.311	-0.2274	0.2537	-0.0762	-0.0388	0.1738	0.0115	0.2497	11.9452	-33.6189	20.969
6	1.4945	0.2056	-0.0585	2.9269	-1.1998	2.9584	0.0589	-0.013	-0.0263	-0.0167	0.0012	0.1069	0.181	-0.0165	-0.0583	0.1207	-0.0028	-0.011	0.1152	0.0042	0.0943	19.7801	-25.2493	23.7833
7	0.9795	-0.0211	-0.1601	1.6768	-0.9528	2.1874	0.0268	0.1386	0.0841	-0.1988	0.0051	0.062	0.1041	-0.08	-0.0291	0.1224	0.01	-0.0124	0.1233	0.0081	0.1179	20.3003	-17.5396	16.0593
8	4.9044	-0.7868	-5.4918	5.1895	0.1793	8.7281	0.3321	0.6171	-1.6434	0.0309	-0.3369	0.2422	0.0286	-1.1849	-0.013	0.2562	-0.0114	-0.0859	0.3603	-0.0126	0.4177	10.6177	-12.5544	-4.7412
9	1.2016	-1.2633	1.0634	3.0491	-1.8709	3.2969	-0.0578	0.0319	0.0904	0.0442	0.0076	-0.0616	-0.3198	0.1652	0.0399	0.183	-0.0376	0.0077	0.1745	0.0224	0.1406	25.0856	-9.0976	9.3997
10	1.5898	-0.8564	0.7244	5.0418	-2.2675	4.1136	-0.0242	-0.0803	-0.1783	0.0754	-0.0236	-0.3106	0.087	0.4096	0.0548	0.1514	0.0469	-0.0001	0.1718	-0.0134	0.1303	31.7491	-27.3954	20.7886
11	3.3434	-0.0868	-2.1967	3.3359	-1.0538	6.385	-0.0609	0.3183	-0.0239	-0.729	0.0288	-0.0765	0.3358	0.0273	0.0053	0.3021	0.022	-0.0228	0.1961	-0.0042	0.1563	24.8816	-27.2306	4.4396
12	6.028	0.8629	-0.3107	4.1658	0.0416	4.3869	0.1586	0.4784	-0.1422	-0.4417	-0.0733	0.3013	0.4498	-0.1604	-0.1176	0.4037	0.0665	-0.0409	0.2019	-0.012	0.172	23.593	-37.0181	9.696
13	3.3954	2.1819	-0.4619	8.1413	-0.9779	3.0644	-0.0709	0.0071	0.2389	0.0113	0.1542	0.3598	-0.1142	-0.0841	-0.0714	0.0932	0.0328	-0.0049	0.1297	0.0189	0.0758	16.1743	-15.1561	43.791
14	0.605	-0.1797	0.2816	2.8028	-1.3686	2.0702	-0.0277	-0.0137	0.0317	0.0129	0.1	0.1328	-0.0514	-0.2053	-0.077	0.0896	0.0081	0.0013	0.136	-0.0036	0.1164	16.2469	-20.0848	40.1185
15	8.0048	3.5513	2.8304	3.871	1.9396	4.2695	0.232	0.0591	-0.1737	0.1681	-0.0541	0.1605	0.7441	-0.2381	-0.1395	0.4309	0.0265	0.0174	0.3042	0.0192	0.1848	12.2982	-31.6658	63.1622
16	1.9539	-0.9671	-1.5213	4.2276	1.9417	3.3865	-0.0472	0.0124	-0.0748	-0.0345	0.0606	-0.0553	0.1252	0.032	-0.0185	0.148	-0.009	-0.0297	0.1221	0.0296	0.1244	25.0576	-34.9269	50.9991
17	8.7478	-0.8505	-4.7123	5.5259	0.2758	2.5538	-0.1371	-0.0064	-0.1249	0.1427	-0.0022	-0.6649	0.3376	0.3559	0.1092	0.1797	0.027	-0.0245	0.2015	0.0292	0.2148	31.457	-31.8997	48.7703
18	1.9103	0.4668	-0.2564	5.0107	-3.0995	3.7714	-0.0181	0.0158	0.0758	0.1529	-0.1543	-0.4158	-0.1637	0.3329	0.2009	0.1185	-0.0051	-0.0104	0.1463	-0.024	0.1742	29.1844	-13.9327	44.0506
19	3.6203	1.5415	2.0584	5.9716	0.882	8.9386	0.0498	-0.2183	0.1114	0.8508	-0.0115	-0.191	-0.2965	0.0417	-0.0409	0.2466	0.0394	-0.027	0.1599	-0.0126	0.1525	23.3703	-12.6163	56.4066

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 205 through 222 )	A	205 - 222
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 223 through 242 )	A	223 - 242
3	X-RAY DIFFRACTION	3	chain 'B' and (resid -3 through 9 )	B	-3 - 9
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 10 through 30 )	B	10 - 30
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 31 through 47 )	B	31 - 47
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 48 through 72 )	B	48 - 72
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 73 through 98 )	B	73 - 98
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 99 through 116 )	B	99 - 116
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 117 through 166 )	B	117 - 166
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 167 through 183 )	B	167 - 183
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 184 through 212 )	B	184 - 212
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 242 )	B	213 - 242
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 0 through 17 )	A	0 - 17
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 18 through 98 )	A	18 - 98
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 99 through 116 )	A	99 - 116
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 117 through 139 )	A	117 - 139
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 140 through 152 )	A	140 - 152
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 153 through 183 )	A	153 - 183
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 184 through 204 )	A	184 - 204

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