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- PDB-3eb9: Crystal structure of 6-phosphogluconolactonase from trypanosoma b... -

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Basic information

Entry
Database: PDB / ID: 3eb9
TitleCrystal structure of 6-phosphogluconolactonase from trypanosoma brucei complexed with citrate
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
CITRATE ANION / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 27, 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.classification / _software.name / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,8696
Polymers57,3602
Non-polymers5094
Water7,710428
1
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers28,6801
Non-polymers2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9343
Polymers28,6801
Non-polymers2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.460, 87.210, 64.790
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number4
Space group name H-MP1211
Details1

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Components

#1: Protein 6-phosphogluconolactonase


Mass: 28679.891 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: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.42 Å3/Da / Density % sol: 49.18 %

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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→24.58 Å / Num. obs: 36055 / % possible obs: 100 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.17 Å2
Reflection shellResolution: 2→2.052 Å

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0E

2j0e


Resolution: 2→24.58 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.149 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1798 4.99 %RANDOM
Rwork0.1953 ---
obs0.1977 36055 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.6311919 Å20 Å2-1.55974903 Å2
2--7.16647457 Å20 Å2
3----1.53528267 Å2
Refinement stepCycle: LAST / Resolution: 2→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 28 428 4401
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01140492
X-RAY DIFFRACTIONt_angle_deg1.2954692
X-RAY DIFFRACTIONt_dihedral_angle_d19.1218350
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013892
X-RAY DIFFRACTIONt_gen_planes0.0185955
X-RAY DIFFRACTIONt_it1.637404920
X-RAY DIFFRACTIONt_nbd0.054605
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2685 283 4.93 %
Rwork0.2026 5460 -
all0.2059 5743 -
obs--97.45 %

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