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- PDB-3k7s: Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B ... -

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Basic information

Entry
Database: PDB / ID: 3k7s
TitleComplex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose 5-phosphate
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / pentose phosphate pathway / Type B ribose 5-phosphate isomerase (RpiB) / R5P
Function / homology
Function and homology information


isomerase activity / carbohydrate metabolic process / identical protein binding
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
5-O-phosphono-D-ribose / Ribose 5-phosphate isomerase / Ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNaworyta, A. / Mowbray, S.L. / Stern, A.L.
CitationJournal: Febs J. / Year: 2011
Title: Structures of type B ribose 5-phosphate isomerase from Trypanosoma cruzi shed light on the determinants of sugar specificity in the structural family.
Authors: Stern, A.L. / Naworyta, A. / Cazzulo, J.J. / Mowbray, S.L.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose 5-phosphate isomerase
B: Ribose 5-phosphate isomerase
C: Ribose 5-phosphate isomerase
D: Ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1588
Polymers78,2374
Non-polymers9204
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-45 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.302, 92.302, 93.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Ribose 5-phosphate isomerase


Mass: 19559.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: strain CL Brener / Gene: 110984573 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A1BTJ7, UniProt: Q4CQE2*PLUS, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-R52 / 5-O-phosphono-D-ribose / Ribose 5-phosphate


Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% (w/v) PEG 550 monomethyl ether, 0.1 M NaCl, 0.1 M Bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→93.659 Å / Num. obs: 63050 / % possible obs: 99.3 %
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K7O

3k7o


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.405 / SU ML: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.196 3203 5.1 %
Rwork0.17 --
obs0.172 63015 99 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 56 474 5194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214986
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9516770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76621.93228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3815826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521558
X-RAY DIFFRACTIONr_chiral_restr0.0740.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23494
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2595
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.53210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84125054
X-RAY DIFFRACTIONr_scbond_it1.39831949
X-RAY DIFFRACTIONr_scangle_it2.3434.51716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.251 226 -
Rwork0.202 4389 -
obs--98.91 %

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