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- PDB-3k7p: Structure of mutant of ribose 5-phosphate isomerase type B from T... -

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Basic information

Entry
Database: PDB / ID: 3k7p
TitleStructure of mutant of ribose 5-phosphate isomerase type B from Trypanosoma cruzi.
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / pentose phosphate pathway / Type B ribose 5-phosphate isomerase (RpiB) / R5P / 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 / Ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)39,2444
Polymers39,0552
Non-polymers1902
Water3,189177
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)78,4898
Polymers78,1094
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9370 Å2
ΔGint-45 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.079, 93.079, 93.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-244-

HOH

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Components

#1: Protein Ribose 5-phosphate isomerase


Mass: 19527.260 Da / Num. of mol.: 2 / Mutation: C69A
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-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.: 177 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.8 M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 79637 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 11.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.1 / Num. unique all: 11693 / Rsym value: 0.335 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.04 Å
Translation2.5 Å33.04 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
DNAdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NN4

1nn4


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.856 / SU B: 1.004 / SU ML: 0.041 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3977 5 %RANDOM
Rwork0.223 ---
all0.223 ---
obs0.223 79570 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.84 Å2 / Biso mean: 16.949 Å2 / Biso min: 8.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 10 177 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212479
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.943369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3045321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72122.143112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61215408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6081526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021906
X-RAY DIFFRACTIONr_nbd_refined0.1810.21237
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0830.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.219
X-RAY DIFFRACTIONr_mcbond_it0.4881.51616
X-RAY DIFFRACTIONr_mcangle_it0.82322539
X-RAY DIFFRACTIONr_scbond_it1.23951
X-RAY DIFFRACTIONr_scangle_it1.9434.5830
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 270 -
Rwork0.278 5645 -
all-5915 -
obs--99.73 %

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