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- PDB-6d24: Trypanosoma cruzi Glucose-6-P Dehydrogenase in complex with G6P -

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Basic information

Entry
Database: PDB / ID: 6d24
TitleTrypanosoma cruzi Glucose-6-P Dehydrogenase in complex with G6P
Components(Glucose-6-phosphate 1- ...) x 2
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / PENTOSE PHOSPHATE PATHWAY / ALPHA BETA / NAD(P) ROSSMANN-LIKE DOMAIN
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 / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.35 Å
AuthorsBotti, H. / Ortiz, C. / Comini, M.A. / Larrieux, N. / Buschiazzo, A.
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: Glucose-6-Phosphate Dehydrogenase from the Human Pathogen Trypanosoma cruzi Evolved Unique Structural Features to Support Efficient Product Formation.
Authors: Ortiz, C. / Botti, H. / Buschiazzo, A. / Comini, M.A.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Expression, crystallization and preliminary X-ray crystallographic analysis of glucose-6-phosphate dehydrogenase from the human pathogen Trypanosoma cruzi in complex with substrate
Authors: Ortiz, C. / Larrieux, N. / Medeiros, A. / Botti, H. / Comini, M. / Buschiazzo, A.
History
DepositionApr 12, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMay 2, 2018ID: 4EM5
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,62062
Polymers243,8414
Non-polymers4,77858
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.790, 133.030, 107.750
Angle α, β, γ (deg.)90.000, 100.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Glucose-6-phosphate 1- ... , 2 types, 4 molecules ABCD

#1: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 60952.293 Da / Num. of mol.: 2 / Mutation: A290E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: G6PDH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1WBU6, glucose-6-phosphate dehydrogenase (NADP+)
#2: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 60968.293 Da / Num. of mol.: 2 / Mutation: A290E
Source method: isolated from a genetically manipulated source
Details: Cys528 oxidized to CSO / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: G6PDH1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1WBU6, glucose-6-phosphate dehydrogenase (NADP+)

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Sugars , 1 types, 4 molecules

#3: Sugar
ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 101 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4 microL 33 mg/mL protein (in 20 mM Tris pH 8.0, 50mM NaCl, 0.5mM MgCl2) plus 4 microL 4% PEG 400, 1.8 M ammonium sulfate, 0.1 M HEPES buffer, 5 mM G6P, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010 / Details: Mirrors: Rh/Pt coated Si
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal [Si(111)]
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→67.359 Å / Num. obs: 38508 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 50.72 Å2 / Rpim(I) all: 0.129 / Rrim(I) all: 0.246 / Rsym value: 0.209 / Net I/av σ(I): 3.3 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.35-3.533.60.451.656060.2770.530.4599.9
3.53-3.753.60.3442.253300.2120.4050.34499.9
3.75-43.50.2433.150120.150.2860.24399.9
4-4.323.50.1883.946510.1160.2220.18899.8
4.32-4.743.50.164.542720.0990.1890.1699.6
4.74-5.33.50.1584.538990.0990.1870.15899.8
5.3-6.123.40.184434010.1170.2190.18499.1
6.12-7.493.10.1385.227910.0930.1670.13895.8
7.49-10.593.70.089622700.0540.1050.089100
10.59-67.3593.60.0915.212760.0550.1070.09199.6

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.35→34.16 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.822 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.526
RfactorNum. reflection% reflectionSelection details
Rfree0.254 796 2.07 %RANDOM
Rwork0.205 ---
obs0.206 38456 99.4 %-
Displacement parametersBiso max: 138.31 Å2 / Biso mean: 36.56 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3543 Å20 Å25.1018 Å2
2---0.6376 Å20 Å2
3---0.2833 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 3.35→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15648 0 256 47 15951
Biso mean--56.98 6.2 -
Num. residues----1992
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5675SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2758HARMONIC5
X-RAY DIFFRACTIONt_it16240HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2096SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18497SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16240HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22026HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion21.27
LS refinement shellResolution: 3.35→3.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2401 54 1.82 %
Rwork0.2038 2920 -
all0.2044 2974 -
obs--99.93 %
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)
13.6246-0.7776-0.68984.72630.55081.68210.0282-0.24130.29670.2460.12740.1984-0.1213-0.1446-0.1556-0.0567-0.04-0.0852-0.1862-0.0614-0.010422.509115.280448.4179
21.3450.41491.20661.3192-0.10231.3033-0.11850.26180.1901-0.10230.1232-0.0756-0.1570.2312-0.0046-0.0099-0.0701-0.1548-0.191-0.0284-0.034518.4118-8.748728.6833
32.5941.1431-1.04824.5345-1.13622.5223-0.0753-0.0355-0.10370.00480.15560.34430.1226-0.2689-0.08030.0078-0.0385-0.1833-0.2532-0.0709-0.0411-0.6201-76.501616.8812
40.1842-0.06670.2551.37380.80411.6163-0.01670.0426-0.14520.0030.2333-0.24230.18230.2146-0.21670.04760.0032-0.1949-0.1589-0.0539-0.061516.9026-52.236126.899
53.2124-1.3526-0.04474.11150.79622.33850.0467-0.29310.2240.0436-0.1153-0.32790.0573-0.03140.0686-0.03680.0211-0.3024-0.1853-0.0086-0.128628.4203-32.59181.6425
61.2353-0.07360.24821.41520.16230.5234-0.0465-0.2258-0.13680.42020.06940.10240.3255-0.0644-0.02290.03990.0402-0.2435-0.15080.0004-0.28284.6428-38.136962.3688
72.33571.15670.00662.8342-1.27052.26490.01190.089-0.0065-0.2447-0.1204-0.10060.182-0.15130.10850.06230.0261-0.2405-0.16130.0284-0.1509-30.5794-28.45731.2142
8-0.2376-0.28310.50791.1875-0.32761.6294-0.0498-0.03780.4507-0.09940.07870.5352-0.1142-0.1679-0.0289-0.12230.0202-0.3181-0.1180.0362-0.2292-19.2371-22.636629.648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|52 - A|246 }A52 - 246
2X-RAY DIFFRACTION2{ A|247 - A|553 A|601 - A|601 }A247 - 553
3X-RAY DIFFRACTION2{ A|247 - A|553 A|601 - A|601 }A601
4X-RAY DIFFRACTION3{ B|52 - B|246 }B52 - 246
5X-RAY DIFFRACTION4{ B|247 - B|553 B|601 - B|601 }B247 - 553
6X-RAY DIFFRACTION4{ B|247 - B|553 B|601 - B|601 }B601
7X-RAY DIFFRACTION5{ C|52 - C|246 }C52 - 246
8X-RAY DIFFRACTION6{ C|247 - C|545 C|601 - C|601 }C247 - 545
9X-RAY DIFFRACTION6{ C|247 - C|545 C|601 - C|601 }C601
10X-RAY DIFFRACTION7{ D|52 - D|246 }D52 - 246
11X-RAY DIFFRACTION8{ D|247 - D|545 D|601 - D|601 }D247 - 545
12X-RAY DIFFRACTION8{ D|247 - D|545 D|601 - D|601 }D601

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