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

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Basic information

Entry
Database: PDB / ID: 4qfh
TitleStructure of a glucose-6-phosphate isomerase from Trypanosoma cruzi
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / 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 / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glucose-6-phosphate isomerase / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2026
Title: Structural Characterization of Glycolytic Enzymes from Trypanosoma cruzi.
Authors: Austin, K. / Obachi, V.A. / Muzenda, F.L. / Moetlediwa, M.T. / Agyei, C. / Craig, T. / Abendroth, J. / Edwards, T. / Nguyen, M. / Tran, N. / Staker, B. / Subramanian, S. / Myler, P. / ...Authors: Austin, K. / Obachi, V.A. / Muzenda, F.L. / Moetlediwa, M.T. / Agyei, C. / Craig, T. / Abendroth, J. / Edwards, T. / Nguyen, M. / Tran, N. / Staker, B. / Subramanian, S. / Myler, P. / Zininga, T. / Govender, K.K. / Chakafana, G.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jul 29, 2020Group: 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 1.3Sep 20, 2023Group: 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
Revision 1.4Mar 4, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4804
Polymers138,9602
Non-polymers5202
Water20,4651136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-85 kcal/mol
Surface area38820 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

#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
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 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 % / Biso Wilson estimate: 16.85 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.67
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.850.5832.31197.9
1.85-1.90.4762.91198
1.9-1.950.3713.71198
1.95-2.010.2914.76198.2
2.01-2.080.2395.74198.3
2.08-2.150.1887.17198.3
2.15-2.230.1528.7198.5
2.23-2.320.1339.75198.7
2.32-2.430.11311.48198.6
2.43-2.550.09812.95198.8
2.55-2.680.08115.3199
2.68-2.850.0717.49199
2.85-3.040.05920.61199.1
3.04-3.290.04824.2199.4
3.29-3.60.03830.17199.3
3.6-4.020.03333.45199.2
4.02-4.650.02937.13199.6
4.65-5.690.02836.27199.5
5.69-8.050.02934.87199.3
8.05-500.02341.2196.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.62 Å46.46 Å
Translation7.62 Å46.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXdev_1702refinement
PDB_EXTRACT3.14data extraction
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1745 5596 5.17 %
Rwork0.1386 --
obs0.1405 108307 98.73 %
all-109888 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.6434 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 32 1136 10716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079910
X-RAY DIFFRACTIONf_angle_d1.01213458
X-RAY DIFFRACTIONf_dihedral_angle_d12.6973642
X-RAY DIFFRACTIONf_chiral_restr0.0421512
X-RAY DIFFRACTIONf_plane_restr0.0051741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.29781800.23453429X-RAY DIFFRACTION98
1.8205-1.84190.2721970.2173369X-RAY DIFFRACTION98
1.8419-1.86440.24671670.20583392X-RAY DIFFRACTION98
1.8644-1.8880.20671880.19493408X-RAY DIFFRACTION98
1.888-1.91280.24982010.18913344X-RAY DIFFRACTION98
1.9128-1.9390.23761910.18593409X-RAY DIFFRACTION98
1.939-1.96670.23951940.17453365X-RAY DIFFRACTION98
1.9667-1.9960.19961890.17183394X-RAY DIFFRACTION98
1.996-2.02720.24641760.16543405X-RAY DIFFRACTION98
2.0272-2.06050.22341990.16593403X-RAY DIFFRACTION98
2.0605-2.0960.19791890.15783410X-RAY DIFFRACTION98
2.096-2.13410.20121630.14823405X-RAY DIFFRACTION98
2.1341-2.17510.19781780.14323403X-RAY DIFFRACTION98
2.1751-2.21950.15681890.13583393X-RAY DIFFRACTION98
2.2195-2.26770.18191760.13283464X-RAY DIFFRACTION99
2.2677-2.32050.17122140.13643384X-RAY DIFFRACTION99
2.3205-2.37850.17611900.13813406X-RAY DIFFRACTION99
2.3785-2.44270.19361750.13973404X-RAY DIFFRACTION99
2.4427-2.51460.20242060.13923434X-RAY DIFFRACTION99
2.5146-2.59570.16631850.13683439X-RAY DIFFRACTION99
2.5957-2.68840.16791780.13493459X-RAY DIFFRACTION99
2.6884-2.7960.18461600.13613476X-RAY DIFFRACTION99
2.796-2.92310.17231760.1383446X-RAY DIFFRACTION99
2.9231-3.07710.17462350.13413381X-RAY DIFFRACTION99
3.0771-3.26960.18151860.1383444X-RAY DIFFRACTION99
3.2696-3.52170.14761920.12223473X-RAY DIFFRACTION99
3.5217-3.87530.13781450.11313510X-RAY DIFFRACTION100
3.8753-4.43440.11891970.10323458X-RAY DIFFRACTION100
4.4344-5.58050.13662020.11323479X-RAY DIFFRACTION100
5.5805-29.19440.14661780.13513525X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.82460.0716-0.01252.17160.02990.55020.0588-0.247-0.04480.2456-0.1282-0.22680.07550.06140.06440.1845-0.0197-0.04540.23840.04020.154940.130827.929228.4909
20.8917-0.1149-0.06751.1913-0.01670.62110.0612-0.1916-0.09720.1865-0.03940.0776-0.0202-0.0309-0.01470.1512-0.02980.02510.19210.01390.09114.075130.917929.5975
31.2226-0.42910.04511.0117-0.47240.9527-0.0039-0.21640.33210.297-0.02360.0802-0.1628-0.04430.06210.22-0.02770.05020.1675-0.08960.231811.348162.984124.5743
40.70650.2736-0.3020.7366-0.41050.8299-0.00120.03480.0739-0.02310.00170.1406-0.0053-0.1199-0.01030.12490.00190.00540.1201-0.00970.190910.751161.40070.9831
50.7823-0.0955-0.08751.5547-1.26182.41580.0560.0050.11480.1307-0.0060.0859-0.2352-0.0171-0.06560.1424-0.00980.00950.1227-0.01720.223517.53672.50851.782
60.6219-0.06730.1441.0172-0.3540.32590.0499-0.14330.13540.1723-0.02880.1155-0.0691-0.0437-0.03020.1464-0.0230.04170.1363-0.04690.119111.076849.90622.265
70.65560.16120.08720.62730.00270.28120.0042-0.04990.0010.039-0.00620.0538-0.02-0.0388-0.00080.1287-0.0120.01450.1455-0.00440.115815.094835.396911.8018
81.4910.13440.01182.46661.61612.59920.07190.1778-0.1954-0.023-0.27590.37380.2515-0.18320.20920.19640.0031-0.0330.144-0.0240.269316.57846.29361.032
90.2084-0.0267-0.03010.8320.04430.27650.0432-0.06520.01330.0891-0.02410.097-0.05440.001-0.01570.1333-0.02150.02110.1453-0.01390.119712.272838.67419.1651
101.94270.6723-1.77731.1743-0.83892.38180.03520.13970.1065-0.0594-0.0046-0.1417-0.1204-0.07-0.04930.1137-0.0097-0.01440.13470.00990.203740.363255.30392.9863
112.1790.60010.65980.66570.85021.11440.0821-0.2282-0.32490.087-0.0034-0.08530.15460.0415-0.07160.15780.0183-0.01410.12680.04720.184439.187516.430416.9474
120.6832-0.03730.12481.06-0.08760.70190.00660.06560.0135-0.037-0.0311-0.265-0.01650.09330.0330.10580.00970.02910.15340.00020.192645.617332.3703-2.7128
131.0137-0.0188-0.13940.661-0.07230.63570.01470.19860.0263-0.1655-0.01080.03380.0002-0.0719-0.00240.1613-0.0026-0.01660.17-0.0080.098812.388635.1513-17.7044
143.2663-0.48570.53141.4089-0.68852.5893-0.01050.3593-0.1706-0.1684-0.00040.17660.0485-0.36660.01640.155-0.033-0.03630.2218-0.03890.175-2.441932.6055-16.8193
150.4740.09350.02390.4827-0.0860.33570.01240.06180.001-0.03730.0001-0.04990.00860.0167-0.00960.11260.00450.01290.1276-0.00370.120729.53437.7851-4.3028
161.27590.98051.03063.60411.28150.92120.2518-0.48870.64910.23390.0284-0.1988-0.55110.3387-0.21430.3032-0.09950.00210.2817-0.1090.314842.650757.515724.8466
170.69910.17010.10110.5995-0.00810.36960.00610.0772-0.0012-0.0278-0.0307-0.0404-0.0130.00360.0210.1035-0.00050.02170.1086-0.0110.10533.839137.42-5.0086
183.47630.3806-1.43820.1607-0.12241.36290.07790.0652-0.01410.0251-0.02090.09010.0431-0.2024-0.04460.1604-0.022-0.00180.13650.0140.19053.799322.35059.2716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 186 )
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 264 )
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 319 )
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 383 )
7X-RAY DIFFRACTION7chain 'A' and (resid 384 through 490 )
8X-RAY DIFFRACTION8chain 'A' and (resid 491 through 519 )
9X-RAY DIFFRACTION9chain 'A' and (resid 520 through 558 )
10X-RAY DIFFRACTION10chain 'A' and (resid 559 through 606 )
11X-RAY DIFFRACTION11chain 'B' and (resid -3 through 54 )
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 134 )
13X-RAY DIFFRACTION13chain 'B' and (resid 135 through 264 )
14X-RAY DIFFRACTION14chain 'B' and (resid 265 through 319 )
15X-RAY DIFFRACTION15chain 'B' and (resid 320 through 490 )
16X-RAY DIFFRACTION16chain 'B' and (resid 491 through 519 )
17X-RAY DIFFRACTION17chain 'B' and (resid 520 through 558 )
18X-RAY DIFFRACTION18chain 'B' and (resid 559 through 606 )

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