PDB-4qfh: Structure of a glucose-6-phosphate isomerase from Trypanosoma cruzi

ID or keywords:

Entry

Database: PDB / ID: 4qfh

Title

Structure of a glucose-6-phosphate isomerase from Trypanosoma cruzi

Components

Glucose-6-phosphate isomerase

Keywords

ISOMERASE / SSGCID /

glucose-6-phosphate isomerase /

Trypanosoma cruzi / Human American trypanosomiasis /

Chagas disease /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glucose-6-phosphate isomerase /

glucose-6-phosphate isomerase activity /

gluconeogenesis / glycolytic process
Similarity search - Function

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Structure of a glucose-6-phosphate isomerase from Trypanosoma cruzi
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lucaks, C. / Lorimer, D. / Edwards, T.E.

History

Deposition	May 21, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4qfh.cif.gz	502.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4qfh.ent.gz	410.8 KB	Display	PDB format
PDBx/mmJSON format	4qfh.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/qf/4qfh ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qfh	HTTPS FTP

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Related structure data

Related structure data	2o2cS S: Starting model for refinement
Similar structure data	2o2c-2 1q50-1 3hjb-2 1gzd-1 3nbu-1 6bzc-d 6bzb-d 1dqr-d 2fhj-d 3hjb-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-TrcrA.17127.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (10) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (9)

Deposited unit

A: Glucose-6-phosphate isomerase

B: Glucose-6-phosphate isomerase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	69.840, 127.030, 72.400
Angle α, β, γ (deg.)	90.00, 109.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Glucose-6-phosphate isomerase /

Mass: 69480.062 Da / Num. of mol.: 2 / Fragment: TrcrA.17127.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053506529.508, TcC31.19 / Plasmid: TrcrA.17127.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O61113, UniProt: Q4E5N1*PLUS,

glucose-6-phosphate isomerase

#2: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.18 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus screen, a8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 30mM of each MgCl2, CaCl2; 0.1 M MOPS/HEPES-Na, TrcrA.17127.a.B1.PS01519 at 25.0 mg/ml with 2.5mM glucose-6- ...Details: Morpheus screen, a8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 30mM of each MgCl2, CaCl2; 0.1 M MOPS/HEPES-Na, TrcrA.17127.a.B1.PS01519 at 25.0 mg/ml with 2.5mM glucose-6-phosphate; tray 251762a8, puck rjo4-3; cryo: direct, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal

Density Matthews: 2.18 Å³/Da / Density % sol: 44 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus screen, a8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 30mM of each MgCl2, CaCl2; 0.1 M MOPS/HEPES-Na, TrcrA.17127.a.B1.PS01519 at 25.0 mg/ml with 2.5mM glucose-6- ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2012

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 109888 / Num. obs: 108344 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.86 % / B_iso Wilson estimate: 16.85 Å² / R_merge(I) obs: 0.077 / Net I/σ(I): 13.67

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.8-1.85	0.583	2.31	1	97.9
1.85-1.9	0.476	2.91	1	98
1.9-1.95	0.371	3.71	1	98
1.95-2.01	0.291	4.76	1	98.2
2.01-2.08	0.239	5.74	1	98.3
2.08-2.15	0.188	7.17	1	98.3
2.15-2.23	0.152	8.7	1	98.5
2.23-2.32	0.133	9.75	1	98.7
2.32-2.43	0.113	11.48	1	98.6
2.43-2.55	0.098	12.95	1	98.8
2.55-2.68	0.081	15.3	1	99
2.68-2.85	0.07	17.49	1	99
2.85-3.04	0.059	20.61	1	99.1
3.04-3.29	0.048	24.2	1	99.4
3.29-3.6	0.038	30.17	1	99.3
3.6-4.02	0.033	33.45	1	99.2
4.02-4.65	0.029	37.13	1	99.6
4.65-5.69	0.028	36.27	1	99.5
5.69-8.05	0.029	34.87	1	99.3
8.05-50	0.023	41.2	1	96.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	7.62 Å	46.46 Å
Translation	7.62 Å	46.46 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.6	phasing
PHENIX	dev_1702	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2o2c

2o2c

Resolution: 1.8→29.191 Å / SU ML: 0.17 / Isotropic thermal model: isotropic TLS / σ(F): 1.36 / Phase error: 17.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1745	5596	5.17 %
R_work	0.1386	-	-
obs	0.1405	108307	98.73 %
all	-	109888	-

Solvent computation

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

Displacement parameters

B_iso mean: 21.6434 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.191 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9548	0	32	1136	10716

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9910
X-RAY DIFFRACTION	f_angle_d	1.012	13458
X-RAY DIFFRACTION	f_dihedral_angle_d	12.697	3642
X-RAY DIFFRACTION	f_chiral_restr	0.042	1512
X-RAY DIFFRACTION	f_plane_restr	0.005	1741

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.8205	0.2978	180	0.2345	3429	X-RAY DIFFRACTION	98
1.8205-1.8419	0.272	197	0.217	3369	X-RAY DIFFRACTION	98
1.8419-1.8644	0.2467	167	0.2058	3392	X-RAY DIFFRACTION	98
1.8644-1.888	0.2067	188	0.1949	3408	X-RAY DIFFRACTION	98
1.888-1.9128	0.2498	201	0.1891	3344	X-RAY DIFFRACTION	98
1.9128-1.939	0.2376	191	0.1859	3409	X-RAY DIFFRACTION	98
1.939-1.9667	0.2395	194	0.1745	3365	X-RAY DIFFRACTION	98
1.9667-1.996	0.1996	189	0.1718	3394	X-RAY DIFFRACTION	98
1.996-2.0272	0.2464	176	0.1654	3405	X-RAY DIFFRACTION	98
2.0272-2.0605	0.2234	199	0.1659	3403	X-RAY DIFFRACTION	98
2.0605-2.096	0.1979	189	0.1578	3410	X-RAY DIFFRACTION	98
2.096-2.1341	0.2012	163	0.1482	3405	X-RAY DIFFRACTION	98
2.1341-2.1751	0.1978	178	0.1432	3403	X-RAY DIFFRACTION	98
2.1751-2.2195	0.1568	189	0.1358	3393	X-RAY DIFFRACTION	98
2.2195-2.2677	0.1819	176	0.1328	3464	X-RAY DIFFRACTION	99
2.2677-2.3205	0.1712	214	0.1364	3384	X-RAY DIFFRACTION	99
2.3205-2.3785	0.1761	190	0.1381	3406	X-RAY DIFFRACTION	99
2.3785-2.4427	0.1936	175	0.1397	3404	X-RAY DIFFRACTION	99
2.4427-2.5146	0.2024	206	0.1392	3434	X-RAY DIFFRACTION	99
2.5146-2.5957	0.1663	185	0.1368	3439	X-RAY DIFFRACTION	99
2.5957-2.6884	0.1679	178	0.1349	3459	X-RAY DIFFRACTION	99
2.6884-2.796	0.1846	160	0.1361	3476	X-RAY DIFFRACTION	99
2.796-2.9231	0.1723	176	0.138	3446	X-RAY DIFFRACTION	99
2.9231-3.0771	0.1746	235	0.1341	3381	X-RAY DIFFRACTION	99
3.0771-3.2696	0.1815	186	0.138	3444	X-RAY DIFFRACTION	99
3.2696-3.5217	0.1476	192	0.1222	3473	X-RAY DIFFRACTION	99
3.5217-3.8753	0.1378	145	0.1131	3510	X-RAY DIFFRACTION	100
3.8753-4.4344	0.1189	197	0.1032	3458	X-RAY DIFFRACTION	100
4.4344-5.5805	0.1366	202	0.1132	3479	X-RAY DIFFRACTION	100
5.5805-29.1944	0.1466	178	0.1351	3525	X-RAY DIFFRACTION	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	0.8246	0.0716	-0.0125	2.1716	0.0299	0.5502	0.0588	-0.247	-0.0448	0.2456	-0.1282	-0.2268	0.0755	0.0614	0.0644	0.1845	-0.0197	-0.0454	0.2384	0.0402	0.1549	40.1308	27.9292	28.4909
2	0.8917	-0.1149	-0.0675	1.1913	-0.0167	0.6211	0.0612	-0.1916	-0.0972	0.1865	-0.0394	0.0776	-0.0202	-0.0309	-0.0147	0.1512	-0.0298	0.0251	0.1921	0.0139	0.091	14.0751	30.9179	29.5975
3	1.2226	-0.4291	0.0451	1.0117	-0.4724	0.9527	-0.0039	-0.2164	0.3321	0.297	-0.0236	0.0802	-0.1628	-0.0443	0.0621	0.22	-0.0277	0.0502	0.1675	-0.0896	0.2318	11.3481	62.9841	24.5743
4	0.7065	0.2736	-0.302	0.7366	-0.4105	0.8299	-0.0012	0.0348	0.0739	-0.0231	0.0017	0.1406	-0.0053	-0.1199	-0.0103	0.1249	0.0019	0.0054	0.1201	-0.0097	0.1909	10.7511	61.4007	0.9831
5	0.7823	-0.0955	-0.0875	1.5547	-1.2618	2.4158	0.056	0.005	0.1148	0.1307	-0.006	0.0859	-0.2352	-0.0171	-0.0656	0.1424	-0.0098	0.0095	0.1227	-0.0172	0.2235	17.536	72.5085	1.782
6	0.6219	-0.0673	0.144	1.0172	-0.354	0.3259	0.0499	-0.1433	0.1354	0.1723	-0.0288	0.1155	-0.0691	-0.0437	-0.0302	0.1464	-0.023	0.0417	0.1363	-0.0469	0.1191	11.0768	49.906	22.265
7	0.6556	0.1612	0.0872	0.6273	0.0027	0.2812	0.0042	-0.0499	0.001	0.039	-0.0062	0.0538	-0.02	-0.0388	-0.0008	0.1287	-0.012	0.0145	0.1455	-0.0044	0.1158	15.0948	35.3969	11.8018
8	1.491	0.1344	0.0118	2.4666	1.6161	2.5992	0.0719	0.1778	-0.1954	-0.023	-0.2759	0.3738	0.2515	-0.1832	0.2092	0.1964	0.0031	-0.033	0.144	-0.024	0.2693	16.5784	6.2936	1.032
9	0.2084	-0.0267	-0.0301	0.832	0.0443	0.2765	0.0432	-0.0652	0.0133	0.0891	-0.0241	0.097	-0.0544	0.001	-0.0157	0.1333	-0.0215	0.0211	0.1453	-0.0139	0.1197	12.2728	38.674	19.1651
10	1.9427	0.6723	-1.7773	1.1743	-0.8389	2.3818	0.0352	0.1397	0.1065	-0.0594	-0.0046	-0.1417	-0.1204	-0.07	-0.0493	0.1137	-0.0097	-0.0144	0.1347	0.0099	0.2037	40.3632	55.3039	2.9863
11	2.179	0.6001	0.6598	0.6657	0.8502	1.1144	0.0821	-0.2282	-0.3249	0.087	-0.0034	-0.0853	0.1546	0.0415	-0.0716	0.1578	0.0183	-0.0141	0.1268	0.0472	0.1844	39.1875	16.4304	16.9474
12	0.6832	-0.0373	0.1248	1.06	-0.0876	0.7019	0.0066	0.0656	0.0135	-0.037	-0.0311	-0.265	-0.0165	0.0933	0.033	0.1058	0.0097	0.0291	0.1534	0.0002	0.1926	45.6173	32.3703	-2.7128
13	1.0137	-0.0188	-0.1394	0.661	-0.0723	0.6357	0.0147	0.1986	0.0263	-0.1655	-0.0108	0.0338	0.0002	-0.0719	-0.0024	0.1613	-0.0026	-0.0166	0.17	-0.008	0.0988	12.3886	35.1513	-17.7044
14	3.2663	-0.4857	0.5314	1.4089	-0.6885	2.5893	-0.0105	0.3593	-0.1706	-0.1684	-0.0004	0.1766	0.0485	-0.3666	0.0164	0.155	-0.033	-0.0363	0.2218	-0.0389	0.175	-2.4419	32.6055	-16.8193
15	0.474	0.0935	0.0239	0.4827	-0.086	0.3357	0.0124	0.0618	0.001	-0.0373	0.0001	-0.0499	0.0086	0.0167	-0.0096	0.1126	0.0045	0.0129	0.1276	-0.0037	0.1207	29.534	37.7851	-4.3028
16	1.2759	0.9805	1.0306	3.6041	1.2815	0.9212	0.2518	-0.4887	0.6491	0.2339	0.0284	-0.1988	-0.5511	0.3387	-0.2143	0.3032	-0.0995	0.0021	0.2817	-0.109	0.3148	42.6507	57.5157	24.8466
17	0.6991	0.1701	0.1011	0.5995	-0.0081	0.3696	0.0061	0.0772	-0.0012	-0.0278	-0.0307	-0.0404	-0.013	0.0036	0.021	0.1035	-0.0005	0.0217	0.1086	-0.011	0.105	33.8391	37.42	-5.0086
18	3.4763	0.3806	-1.4382	0.1607	-0.1224	1.3629	0.0779	0.0652	-0.0141	0.0251	-0.0209	0.0901	0.0431	-0.2024	-0.0446	0.1604	-0.022	-0.0018	0.1365	0.014	0.1905	3.7993	22.3505	9.2716

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 134 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 186 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 187 through 264 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 265 through 319 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 383 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 384 through 490 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 491 through 519 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 520 through 558 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 559 through 606 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -3 through 54 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 55 through 134 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 135 through 264 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 265 through 319 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 320 through 490 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 491 through 519 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 520 through 558 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 559 through 606 )

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