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- PDB-3ch7: Crystal structure of 6-phosphogluconolactonase from Leishmania br... -

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Basic information

Entry
Database: PDB / ID: 3ch7
TitleCrystal structure of 6-phosphogluconolactonase from Leishmania braziliensis
Components6-phosphogluconolactonase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / 6-phosphogluconolactonase / leishmaniasis / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
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
6-phosphogluconolactonase
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: to be published
Title: 6-phosphogluconolactonase from Leishmania braziliensis.
Authors: Arakaki, T.L. / Merritt, E.A.
History
DepositionMar 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphogluconolactonase


Theoretical massNumber of molelcules
Total (without water)28,5581
Polymers28,5581
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.967, 88.490, 100.523
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 6-phosphogluconolactonase


Mass: 28557.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Strain: MHOM/BR/75/M2904 / Gene: Lbra003394AAA, LbrM26_V2.2630 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4HFB4, gluconolactonase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE DIFFERENCES BETWEEN THE SEQUENCE OF THEIR PROTEIN AND THE UNIPROT SEQUENCE ...AUTHORS STATE THAT THE DIFFERENCES BETWEEN THE SEQUENCE OF THEIR PROTEIN AND THE UNIPROT SEQUENCE ARE DUE TO STRAIN VARIATIONS.

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 40% PEG 1000, 0.1 M MOPS, 0.1 M NH4H2PO4, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 13.9 / Number: 96585 / Rmerge(I) obs: 0.069 / Χ2: 1.01 / D res high: 2.29 Å / D res low: 50 Å / Num. obs: 13966 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.935099.810.0350.9856.9
3.924.9310010.0551.0117.3
3.423.9210010.0660.9937.4
3.113.4210010.0841.0417.4
2.893.1110010.1171.0117.4
2.722.8910010.161.0197.4
2.582.729910.2061.0287
2.472.589610.290.9826.5
2.372.478810.2711.0546.1
2.292.378210.3381.0445.4
ReflectionResolution: 2.29→50 Å / Num. obs: 13966 / % possible obs: 96.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.069 / Χ2: 1.015 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.29-2.375.40.33811741.044182
2.37-2.476.10.27112451.054188
2.47-2.586.50.2913770.982196
2.58-2.7270.20614081.028199
2.72-2.897.40.1614111.0191100
2.89-3.117.40.11714361.0111100
3.11-3.427.40.08414421.0411100
3.42-3.927.40.06614520.9931100
3.92-4.937.30.05514741.0111100
4.93-506.90.03515470.985199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.55 Å37.07 Å
Translation2.55 Å37.07 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.4.0066refinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2J0E

2j0e


Resolution: 2.29→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.951 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 698 5 %RANDOM
Rwork0.19 ---
obs0.192 13964 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.788 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--2.44 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.29→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 74 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222074
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9762827
X-RAY DIFFRACTIONr_angle_other_deg1.01233426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43724.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1041513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_mcbond_it1.97321342
X-RAY DIFFRACTIONr_mcbond_other0.4992538
X-RAY DIFFRACTIONr_mcangle_it3.21132175
X-RAY DIFFRACTIONr_scbond_it2.4962732
X-RAY DIFFRACTIONr_scangle_it44647
LS refinement shellResolution: 2.29→2.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 52 -
Rwork0.252 797 -
all-849 -
obs--79.49 %

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