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- PDB-6vye: 6-phosphogluconolactonase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 6vye
Title6-phosphogluconolactonase from Trypanosoma cruzi
Components6-phosphogluconolactonase
KeywordsHYDROLASE / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / carbohydrate metabolic process
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
PHOSPHATE ION / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMerritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be published
Title: 6-phosphogluconolactonase from Trypanosoma cruzi
Authors: Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) / Hol, W.G.J. / Buckner, F.S. / Van Voorhis, W.C. / Neely, H. / Le Trong, I. / Caruthers, J. / Fan, E. / Verlinde, C.L.M.J.
History
DepositionFeb 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: 6-phosphogluconolactonase
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9748
Polymers59,4132
Non-polymers5616
Water3,891216
1
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0815
Polymers29,7071
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8943
Polymers29,7071
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.770, 63.390, 79.320
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-301-

PO4

21B-464-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#1: Protein 6-phosphogluconolactonase / 6PGL


Mass: 29706.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053503945.40 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4CQA8, 6-phosphogluconolactonase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.1 M sodium citrate, 3.5 mM DTT, cryo-soak in 30% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→50.9 Å / Num. obs: 49639 / % possible obs: 95.8 % / Redundancy: 3.6 % / CC1/2: 0.971 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.15 / Rrim(I) all: 0.288 / Net I/σ(I): 4.9 / Num. measured all: 179047 / Scaling rejects: 1547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.11.669883328510.4721.1062.014177.7
8.94-50.93.20.06617115360.9930.0430.07911.793

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eb9

3eb9


Resolution: 1.95→49.497 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.412 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions Babinet solvent model
RfactorNum. reflection% reflection
Rfree0.2699 2543 5.132 %
Rwork0.2312 --
all0.233 --
obs-49552 95.329 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.828 Å2
Baniso -1Baniso -2Baniso -3
1-1.496 Å20 Å2-0.389 Å2
2---2.648 Å2-0 Å2
3---1.201 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 33 216 4308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134177
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174035
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6325659
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5739372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67722.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49515735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8931522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
X-RAY DIFFRACTIONr_nbd_refined0.2130.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23781
X-RAY DIFFRACTIONr_nbtor_refined0.1510.21977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2188
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.236
X-RAY DIFFRACTIONr_nbd_other0.2150.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.235
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_mcbond_it2.1852.5192122
X-RAY DIFFRACTIONr_mcbond_other2.1842.5162121
X-RAY DIFFRACTIONr_mcangle_it3.5093.7582649
X-RAY DIFFRACTIONr_mcangle_other3.5083.7622650
X-RAY DIFFRACTIONr_scbond_it2.6882.7542052
X-RAY DIFFRACTIONr_scbond_other2.6882.7552053
X-RAY DIFFRACTIONr_scangle_it4.2213.9993008
X-RAY DIFFRACTIONr_scangle_other4.2243009
X-RAY DIFFRACTIONr_lrange_it6.4929.814457
X-RAY DIFFRACTIONr_lrange_other6.4929.8114458
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.058192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3431510.3492837X-RAY DIFFRACTION77.8531
2.001-2.0550.3582030.3273322X-RAY DIFFRACTION95.0647
2.055-2.1150.3351950.3173302X-RAY DIFFRACTION95.9133
2.115-2.180.3191370.2993242X-RAY DIFFRACTION96.3502
2.18-2.2510.3181770.273107X-RAY DIFFRACTION96.2768
2.251-2.330.3121490.2693033X-RAY DIFFRACTION96.2201
2.33-2.4180.3271480.2542926X-RAY DIFFRACTION97.1248
2.418-2.5170.2961580.232808X-RAY DIFFRACTION96.7384
2.517-2.6290.2691440.2222707X-RAY DIFFRACTION97.0718
2.629-2.7570.2371360.2122629X-RAY DIFFRACTION97.2564
2.757-2.9060.2691300.2072469X-RAY DIFFRACTION97.1952
2.906-3.0820.2391200.1882356X-RAY DIFFRACTION97.4803
3.082-3.2940.2371230.1882218X-RAY DIFFRACTION97.5417
3.294-3.5580.231290.1982046X-RAY DIFFRACTION97.973
3.558-3.8960.2261070.1941892X-RAY DIFFRACTION97.7984
3.896-4.3550.2311060.1861704X-RAY DIFFRACTION97.3642
4.355-5.0260.258890.21537X-RAY DIFFRACTION97.4236
5.026-6.150.219550.2281305X-RAY DIFFRACTION97.7714
6.15-8.6710.292570.2161010X-RAY DIFFRACTION95.781
8.671-49.4970.19290.234559X-RAY DIFFRACTION91.875

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