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- PDB-6fxw: Structure of Leishmania infantum type B ribose 5-phosphate isomerase -

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Basic information

Entry
Database: PDB / ID: 6fxw
TitleStructure of Leishmania infantum type B ribose 5-phosphate isomerase
ComponentsPutative ribose 5-phosphate isomerase
KeywordsISOMERASE / PENTOSE PHOSPHATE PATHWAY TYPE B RIBOSE 5-PHOSPHATE ISOMERASE R5P
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / carbohydrate metabolic process
Similarity search - Function
Ribose 5-phosphate isomerase B / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRonin, C. / Ciesielski, F. / Ciapetti, P.
Funding support France, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme602773 France
CitationJournal: Antimicrob.Agents Chemother. / Year: 2021
Title: Toward Chemical Validation of Leishmania infantum Ribose 5-Phosphate Isomerase as a Drug Target.
Authors: Dickie, E.A. / Ronin, C. / Sa, M. / Ciesielski, F. / Trouche, N. / Tavares, J. / Santarem, N. / Major, L.L. / Pemberton, I.K. / MacDougall, J. / Smith, T.K. / Cordeiro-da-Silva, A. / Ciapetti, P.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1663
Polymers18,9741
Non-polymers1922
Water1,65792
1
A: Putative ribose 5-phosphate isomerase
hetero molecules

A: Putative ribose 5-phosphate isomerase
hetero molecules

A: Putative ribose 5-phosphate isomerase
hetero molecules

A: Putative ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,66312
Polymers75,8944
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y+1/2,-z-1/21
crystal symmetry operation11_454-x-1/2,y,-z-1/21
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area10820 Å2
ΔGint-148 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.920, 83.650, 89.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-390-

HOH

31A-392-

HOH

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Components

#1: Protein Putative ribose 5-phosphate isomerase


Mass: 18973.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINJ_28_2100 / Production host: Escherichia coli (E. coli) / References: UniProt: A4I3S4, ribose-5-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7; 2M NH4SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.912 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.57→19.75 Å / Num. obs: 21306 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rsym value: 0.0527 / Net I/σ(I): 23.2
Reflection shellResolution: 1.57→1.66 Å / Mean I/σ(I) obs: 5.09 / Rsym value: 0.343 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k7o

3k7o


Resolution: 1.57→19.75 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.207 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17829 1066 5 %RANDOM
Rwork0.14439 ---
obs0.14611 20240 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.57→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 10 92 1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191202
X-RAY DIFFRACTIONr_bond_other_d0.0020.021114
X-RAY DIFFRACTIONr_angle_refined_deg2.2171.9611635
X-RAY DIFFRACTIONr_angle_other_deg1.13932590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65724.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16215210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.196158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021356
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02228
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0461.526623
X-RAY DIFFRACTIONr_mcbond_other1.9591.518622
X-RAY DIFFRACTIONr_mcangle_it2.9472.277780
X-RAY DIFFRACTIONr_mcangle_other2.9582.285781
X-RAY DIFFRACTIONr_scbond_it3.211.878579
X-RAY DIFFRACTIONr_scbond_other3.2151.872572
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8312.663838
X-RAY DIFFRACTIONr_long_range_B_refined5.70119.1211330
X-RAY DIFFRACTIONr_long_range_B_other5.69118.9431319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.569→1.609 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 74 -
Rwork0.269 1407 -
obs--94.94 %

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