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- PDB-3e15: 6-phosphogluconolactonase from Plasmodium vivax -

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Basic information

Entry
Database: PDB / ID: 3.0E+15
Title6-phosphogluconolactonase from Plasmodium vivax
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsHYDROLASE / 6-phosphogluconolactonase / malaria / Carbohydrate metabolism / Glucose metabolism / NADP / Oxidoreductase
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase activity / glucose metabolic process / NADP binding
Similarity search - Function
Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / 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 / Rossmann fold - #1360 / NagB/RpiA transferase-like / NAD(P)-binding domain superfamily ...Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / 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 / Rossmann fold - #1360 / NagB/RpiA transferase-like / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / : / Glucose-6-phosphate 1-dehydrogenase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsArakaki, T.L. / Merritt, E.A.
CitationJournal: To be Published
Title: 6-phosphogluconolactonase from Plasmodium vivax
Authors: Arakaki, T.L. / Merritt, E.A.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)147,06914
Polymers146,6744
Non-polymers39510
Water13,547752
1
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5347
Polymers73,3372
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-20 kcal/mol
Surface area24890 Å2
MethodPISA
2
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

C: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5347
Polymers73,3372
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3510 Å2
ΔGint-19 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.524, 80.846, 89.765
Angle α, β, γ (deg.)63.980, 88.100, 80.010
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36668.391 Da / Num. of mol.: 4
Fragment: structures 1-304, 6-phosphogluconolactonase domain
Source method: isolated from a genetically manipulated source
Details: Pviv003883AAE PlasmoDB PB001310.02.0
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_117790 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: A5K3M1, 6-phosphogluconolactonase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 17% PEG 1000, 0.1 M potassium chloride, 0.1 M sodium acetate, 5 mM DTT, pH 5.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9797 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 11, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→80.582 Å / Num. obs: 76585 / % possible obs: 98 % / Redundancy: 4 % / Rmerge(I) obs: 0.045

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
SOLVE2.12phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.854 / SU B: 3.153 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3839 5 %RANDOM
Rwork0.15 ---
obs0.152 76395 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.52 Å2 / Biso mean: 18.272 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0.15 Å20.04 Å2
2---0.02 Å20.61 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9740 0 18 752 10510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229963
X-RAY DIFFRACTIONr_bond_other_d0.0010.026621
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.95913498
X-RAY DIFFRACTIONr_angle_other_deg0.79316313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8951225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.525.544487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.755151863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8041524
X-RAY DIFFRACTIONr_chiral_restr0.0840.21523
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210960
X-RAY DIFFRACTIONr_gen_planes_other00.021956
X-RAY DIFFRACTIONr_mcbond_it1.1241.55946
X-RAY DIFFRACTIONr_mcbond_other0.3411.52394
X-RAY DIFFRACTIONr_mcangle_it1.99829698
X-RAY DIFFRACTIONr_scbond_it3.15334017
X-RAY DIFFRACTIONr_scangle_it4.8664.53770
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 295 -
Rwork0.138 5248 -
all-5543 -
obs--96.12 %

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