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- PDB-3m1p: Structure of ribose 5-phosphate isomerase type B from Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 3m1p
TitleStructure of ribose 5-phosphate isomerase type B from Trypanosoma cruzi, soaked with allose-6-phosphate
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / type B ribose 5-phosphate isomerase / allose-6-phosphate
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
PHOSPHATE ION / Ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMar 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)33,7024
Polymers33,5122
Non-polymers1902
Water2,450136
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)67,4058
Polymers67,0254
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9430 Å2
ΔGint-43 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.763, 92.763, 93.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ribose 5-phosphate isomerase


Mass: 16756.166 Da / Num. of mol.: 2 / Mutation: C69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053509199.24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4CQE2, ribose-5-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG3350, 0.2M sodium acetate, 0.1 M BIS-TRIS propane, pH 8.5, VAPOR DIFFUSION, 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 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→65.71 Å / Num. all: 18940 / Num. obs: 18940 / % possible obs: 90.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.326.50.2682.81835128020.26892.6
2.32-2.466.60.2393.11711126060.23992.1
2.46-2.636.60.1794.11631824900.17991.6
2.63-2.846.50.1534.71490822780.15391.1
2.84-3.116.50.135.31372721050.1390.3
3.11-3.486.50.1026.51223118850.10289.3
3.48-4.026.30.087.91039516570.0888.5
4.02-4.9260.0629.3827413830.06285.9
4.92-6.966.90.05910.4764511090.05986.4
6.96-29.426.50.03815.340486250.03883

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 4.712 / SU ML: 0.122 / SU R Cruickshank DPI: 0.253 / SU Rfree: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 978 5.2 %RANDOM
Rwork0.187 ---
obs0.189 18909 89.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.76 Å2 / Biso mean: 21.072 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 10 136 2486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212501
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9393398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90621.826115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6115415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0611529
X-RAY DIFFRACTIONr_chiral_restr0.0770.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021929
X-RAY DIFFRACTIONr_nbd_refined0.1970.21316
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_mcbond_it0.5921.51625
X-RAY DIFFRACTIONr_mcangle_it1.00222550
X-RAY DIFFRACTIONr_scbond_it1.4693968
X-RAY DIFFRACTIONr_scangle_it2.3934.5848
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 67 -
Rwork0.187 1340 -
all-1407 -
obs--91.84 %

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