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- PDB-3e7f: Crystal structure of 6-phosphogluconolactonase from Trypanosoma b... -

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Basic information

Entry
Database: PDB / ID: 3e7f
TitleCrystal structure of 6-phosphogluconolactonase from Trypanosoma brucei complexed with 6-phosphogluconic acid
Components6-phosphogluconolactonase
KeywordsHYDROLASE / CATALYTIC MECHANISM / PENTOSE PHOSPHATE PATHWAY / 6-PHOSPHOGLUCONOLACTONASE / TRYPANOSOMA BRUCEI / ZINC BINDING SITE
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / glycosome / pentose-phosphate shunt / carbohydrate metabolic process / metal ion binding / cytoplasm
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsPoggi, L. / Delarue, M. / Duclert-Savatier, N. / Stoven, V.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation.
Authors: Duclert-Savatier, N. / Poggi, L. / Miclet, E. / Lopes, P. / Ouazzani, J. / Chevalier, N. / Nilges, M. / Delarue, M. / Stoven, V.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconolactonase
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7806
Polymers57,0972
Non-polymers6834
Water7,764431
1
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8903
Polymers28,5491
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8903
Polymers28,5491
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.660, 87.000, 64.910
Angle α, β, γ (deg.)90.00, 96.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 6-phosphogluconolactonase


Mass: 28548.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: 6pgl / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9GRG6, gluconolactonase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.44 Å3/Da / Density % sol: 49.65 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→24 Å / Num. all: 27717 / Num. obs: 27717 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.013 Å2
Reflection shellResolution: 2.2→2.5 Å / % possible all: 86.6

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Processing

Software
NameVersionClassificationNB
BUSTER-TNT2.1.1refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
RefinementResolution: 2.2→23.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.198 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1393 5.03 %RANDOM
Rwork0.1738 ---
obs0.1776 27717 99.17 %-
all-27716 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.21 Å2
Baniso -1Baniso -2Baniso -3
1--6.19098368 Å20 Å2-3.92252768 Å2
2--7.60675712 Å20 Å2
3----1.41577344 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 36 431 4404
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01140472
X-RAY DIFFRACTIONt_angle_deg1.30254722
X-RAY DIFFRACTIONt_dihedral_angle_d20.3598350
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011892
X-RAY DIFFRACTIONt_gen_planes0.0175925
X-RAY DIFFRACTIONt_it1.692404720
X-RAY DIFFRACTIONt_nbd0.051775
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2894 217 4.97 %
Rwork0.2093 4152 -
all0.2132 4369 -
obs--99.17 %

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