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- PDB-5aq1: Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5aq1
TitleTrypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH
ComponentsGLUCOSE-6-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PENTOSE PHOSPHATE PATHWAY / REDOX BALANCE / CHAGAS DISEASE / G6PD / G6PDH.
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / Chem-NDP / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMercaldi, G.F. / Dawson, A. / Hunter, W.N. / Cordeiro, A.T.
CitationJournal: FEBS Lett. / Year: 2016
Title: The Structure of a Trypanosoma Cruzi Glucose-6-Phosphate Dehydrogenase Reveals Differences from the Mammalian Enzyme.
Authors: Mercaldi, G.F. / Dawson, A. / Hunter, W.N. / Cordeiro, A.T.
History
DepositionSep 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8789
Polymers172,8613
Non-polymers3,0176
Water4,558253
1
B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,50412
Polymers230,4824
Non-polymers4,0228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area15460 Å2
ΔGint-89.5 kcal/mol
Surface area94800 Å2
MethodPQS
2
A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,50412
Polymers230,4824
Non-polymers4,0228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
crystal symmetry operation10_675-x+1,-y+2,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
Buried area15440 Å2
ΔGint-74.7 kcal/mol
Surface area94120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)154.946, 154.946, 348.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein GLUCOSE-6-PHOSPHATE DEHYDROGENASE /


Mass: 57620.449 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 58-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: CL BRENER / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4E0B2, glucose-6-phosphate dehydrogenase (NADP+)
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTRUNCATED CONSTRUCT WITH 57 AMINOACIDS IN N TERMINUS AND 10 AMINOACIDS IN C TERMINUS REMOVED.

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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: 3.03 Å3/Da / Density % sol: 59.35 % / Description: NONE
Crystal growDetails: PROTEIN: 2UL TCG6PD 10MG/ML, 5MM G6P, 2 MM NADPH; BUFFER: 20 MM TRIS PH 8.0 WITH 0.2 M NACL AND 5 MM ME PRECIPITANT: 1 UL JEFFAMINE ED-2003 PH 7.0 30%, 0.1 M HEPES PH 7.0;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 2.65→49.13 Å / Num. obs: 58510 / % possible obs: 95.4 % / Observed criterion σ(I): 2.5 / Redundancy: 8.7 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E9I

4e9i
PDB Unreleased entry


Resolution: 2.65→141.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.601 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.694 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22553 2941 5 %RANDOM
Rwork0.19991 ---
obs0.20118 55569 94.73 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→141.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11571 0 192 253 12016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912018
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211475
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.98516290
X-RAY DIFFRACTIONr_angle_other_deg0.808326355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53251449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9323.158570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.113152064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.07515117
X-RAY DIFFRACTIONr_chiral_restr0.0560.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022829
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5442.5315805
X-RAY DIFFRACTIONr_mcbond_other1.5442.535804
X-RAY DIFFRACTIONr_mcangle_it2.7253.7897251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8042.8196212
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 223 -
Rwork0.311 4141 -
obs--96.57 %
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)
10.78370.4186-0.07991.2756-0.07520.6584-0.01640.037-0.2146-0.1162-0.0184-0.10570.25880.02850.03470.13680.03530.01810.0198-0.00070.200276.09122.5875.311
20.709-0.50510.13231.4416-0.15960.518-0.0232-0.06230.17810.15060.0314-0.1294-0.0925-0.0092-0.00820.1462-0.033400.0862-0.00810.263476.261109.68124.929
31.1693-0.4256-0.20581.0040.09120.8985-0.05360.05570.0927-0.02280.0448-0.32890.00290.36860.00870.15-0.0411-0.00030.223-0.0130.3341109.97175.249101.35
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 545
2X-RAY DIFFRACTION2B62 - 545
3X-RAY DIFFRACTION3C62 - 545

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