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- PDB-6fxs: Structure of Trypanosoma brucei type B ribose 5-phosphate isomerase -

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Basic information

Entry
Database: PDB / ID: 6fxs
TitleStructure of Trypanosoma brucei type B ribose 5-phosphate isomerase
Components(Ribose 5-phosphate isomerase, putative) x 2
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 / pentose-phosphate shunt, non-oxidative branch / glycosome / isomerase activity / carbohydrate metabolic process / mitochondrion
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
Ribose 5-phosphate isomerase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRonin, C. / Ciesielski, F. / Ciapetti, P.
Funding support France, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme602773 France
CitationJournal: To Be Published
Title: Structure of Trypanosoma brucei type B ribose 5-phosphate isomerase (TbRpiB)
Authors: Ronin, C. / Ciesielski, F. / 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribose 5-phosphate isomerase, putative
B: Ribose 5-phosphate isomerase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6225
Polymers38,3332
Non-polymers2883
Water2,576143
1
A: Ribose 5-phosphate isomerase, putative
B: Ribose 5-phosphate isomerase, putative
hetero molecules

A: Ribose 5-phosphate isomerase, putative
B: Ribose 5-phosphate isomerase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,24310
Polymers76,6674
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area10460 Å2
ΔGint-152 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 97.800, 84.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Ribose 5-phosphate isomerase, putative


Mass: 19182.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.01.0700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q384D1, ribose-5-phosphate isomerase
#2: Protein Ribose 5-phosphate isomerase, putative


Mass: 19150.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.01.0700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q384D1, ribose-5-phosphate isomerase
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100mM hepes pH7.5; 1.26M 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: 2.01→19.56 Å / Num. obs: 27783 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rsym value: 0.111 / Net I/σ(I): 22.12
Reflection shellResolution: 2.01→2.13 Å / Mean I/σ(I) obs: 4.45 / Rsym value: 0.627 / % possible all: 99.5

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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: 2.01→19.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.901 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19774 1390 5 %RANDOM
Rwork0.16394 ---
obs0.16565 26392 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.01→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 15 143 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192358
X-RAY DIFFRACTIONr_bond_other_d0.0020.022209
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.963195
X-RAY DIFFRACTIONr_angle_other_deg1.12535089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42922.593108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.761524
X-RAY DIFFRACTIONr_chiral_restr0.1230.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
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_it2.1472.0951192
X-RAY DIFFRACTIONr_mcbond_other2.1422.0911191
X-RAY DIFFRACTIONr_mcangle_it2.9363.1191487
X-RAY DIFFRACTIONr_mcangle_other2.9393.1231488
X-RAY DIFFRACTIONr_scbond_it3.9182.6291166
X-RAY DIFFRACTIONr_scbond_other3.9152.6091154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8343.7211689
X-RAY DIFFRACTIONr_long_range_B_refined6.80926.352629
X-RAY DIFFRACTIONr_long_range_B_other6.79226.1712601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.009→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 99 -
Rwork0.462 1879 -
obs--98.95 %

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