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- PDB-6d23: GLUCOSE-6-P DEHYDROGENASE (APO FORM) FROM TRYPANOSOMA CRUZI -

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Basic information

Entry
Database: PDB / ID: 6d23
TitleGLUCOSE-6-P DEHYDROGENASE (APO FORM) FROM TRYPANOSOMA CRUZI
ComponentsGlucose-6-phosphate 1-dehydrogenase
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
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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: 4E9I
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Structure summary / Category: audit_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 1.4Oct 4, 2023Group: 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

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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)248,77271
Polymers243,8094
Non-polymers4,96367
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26900 Å2
ΔGint-547 kcal/mol
Surface area74290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.610, 132.960, 107.830
Angle α, β, γ (deg.)90.000, 100.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60952.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli)
References: UniProt: Q1WBU6, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4 microL 20 mg/mL protein (in 20 mM Tris pH8.0, 50mM NaCl, 0.5mM MgCl2), plus 4 microL 6% PEG 400, 1.6 M ammonium sulfate, 0.1 M HEPES 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: 2.85→29.629 Å / Num. obs: 62028 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.17 Å2 / Rpim(I) all: 0.086 / Rrim(I) all: 0.163 / Rsym value: 0.138 / Net I/av σ(I): 4.8 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.85-33.40.5011.590280.3160.5940.50199.2
3-3.193.40.3562.285410.2240.4210.35699.2
3.19-3.413.50.2213.480780.1380.2620.22199.4
3.41-3.683.50.1564.375040.0970.1840.15699.3
3.68-4.033.60.118668970.0730.1390.11899.2
4.03-4.513.50.0877.962310.0540.1020.08799.2
4.51-5.23.50.0877.655250.0540.1030.08799.4
5.2-6.373.40.1016.546670.0640.1190.10199
6.37-9.013.30.0717.735680.0450.0840.07197.2
9.01-29.6293.70.0835.919890.050.0970.08397.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QKI

1qki


Resolution: 2.85→29.629 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.774 / SU Rfree Blow DPI: 0.344
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1257 2.03 %RANDOM
Rwork0.204 ---
obs0.205 62009 99 %-
Displacement parametersBiso max: 133.56 Å2 / Biso mean: 44.35 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--7.1148 Å20 Å27.9382 Å2
2--6.2455 Å20 Å2
3---0.8694 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.85→29.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15441 0 263 75 15779
Biso mean--67 25.43 -
Num. residues----1965
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5592SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2722HARMONIC5
X-RAY DIFFRACTIONt_it16036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2053SEMIHARMONIC5
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_contact17828SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16036HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg21733HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion20.35
LS refinement shellResolution: 2.85→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 102 2.23 %
Rwork0.2221 4471 -
all0.2227 4573 -
obs--99 %
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)
13.52020.099-0.253.2980.04761.83660.0029-0.48270.51680.52210.21820.2392-0.4245-0.0022-0.221-0.13-0.0680.059-0.257-0.136-0.067323.240614.918648.6348
21.42330.55240.57251.19490.19421.0179-0.19160.28780.2585-0.17610.2242-0.1207-0.23520.2973-0.0327-0.1457-0.0749-0.0487-0.1156-0.0054-0.049418.479-9.191329.0565
32.02721.3242-0.99023.9337-0.94732.6929-0.12880.1227-0.1638-0.17760.31730.66270.2292-0.3431-0.1886-0.1152-0.0435-0.0218-0.2038-0.0648-0.1166-0.5672-76.491916.2156
40.89770.00030.40041.40080.75471.6832-0.04890.1658-0.1711-0.03760.2526-0.27130.26950.304-0.2037-0.06660.0276-0.0169-0.133-0.0715-0.125816.7384-52.340726.7954
54.4789-1.12150.22442.48090.07071.906-0.0639-0.60740.33440.1778-0.0797-0.54960.0828-0.02580.1436-0.16830.1063-0.2022-0.0885-0.0645-0.233928.6453-32.839881.5748
60.860.07050.26921.45870.38291.5155-0.102-0.1838-0.09440.39880.11250.03480.33-0.0108-0.0105-0.010.1304-0.0536-0.13280.0046-0.17874.6424-38.317162.3134
71.93410.5472-0.72072.5822-0.7663.942-0.06220.16160.001-0.61-0.0344-0.01580.3429-0.54160.0966-0.1523-0.0894-0.1694-0.07520.0823-0.2595-30.2164-28.821.2619
81.0990.33180.49451.39050.10281.1252-0.11520.02420.3311-0.11820.08510.3957-0.1318-0.24290.0302-0.136-0.0085-0.0933-0.11960.0996-0.0334-19.2011-22.927929.7639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|59 - A|246 }A59 - 246
2X-RAY DIFFRACTION2{ A|247 - A|545 }A247 - 545
3X-RAY DIFFRACTION3{ B|56 - B|246 }B56 - 246
4X-RAY DIFFRACTION4{ B|247 - B|545 }B247 - 545
5X-RAY DIFFRACTION5{ C|52 - C|246 }C52 - 246
6X-RAY DIFFRACTION6{ C|247 - C|545 }C247 - 545
7X-RAY DIFFRACTION7{ D|52 - D|246 }D52 - 246
8X-RAY DIFFRACTION8{ D|247 - D|545 }D247 - 545

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