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- PDB-3k8c: Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B ... -

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Basic information

Entry
Database: PDB / ID: 3k8c
TitleComplex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with 4-deoxy-4-phospho-D-erythronohydroxamic acid
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / pentose phosphate pathway / Type B ribose 5-phosphate isomerase (RpiB) / 4PEH / 4-deoxy-4-phospho-D-erythronohydroxamic acid
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
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID / Ribose 5-phosphate isomerase / Ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5814
Polymers39,1192
Non-polymers4622
Water1,62190
1
A: Ribose 5-phosphate isomerase
B: Ribose 5-phosphate isomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)79,1628
Polymers78,2374
Non-polymers9244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9340 Å2
ΔGint-45 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.387, 92.387, 94.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ribose 5-phosphate isomerase


Mass: 19559.324 Da / Num. of mol.: 2
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-RES / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID


Mass: 231.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) PEG 6000, 0.2 M ammonium chloride, 0.1 M Tris-HCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→65.938 Å / Num. obs: 23175 / % possible obs: 96 % / Observed criterion σ(F): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.451 / % possible all: 95.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K7P

3k7p


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.474 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 1.579 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25336 1194 5.2 %RANDOM
Rwork0.21674 ---
obs0.21859 21960 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 28 90 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9523301
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42922.252111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21238
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21654
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1421.51581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97622465
X-RAY DIFFRACTIONr_scbond_it2.3353951
X-RAY DIFFRACTIONr_scangle_it3.5244.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 107 -
Rwork0.291 1556 -
obs--95.19 %

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