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- PDB-1xtz: Crystal structure of the S. cerevisiae D-ribose-5-phosphate isome... -

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Basic information

Entry
Database: PDB / ID: 1xtz
TitleCrystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archeal and bacterial enzymes
ComponentsRibose-5-phosphate isomerase
KeywordsISOMERASE / D-ribose-5-phosphate isomerase / yeast
Function / homology
Function and homology information


Pentose phosphate pathway / D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pyridoxine biosynthetic process / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / intracellular membrane-bounded organelle / nucleus / cytoplasm
Similarity search - Function
Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose-5-phosphate isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGraille, M. / Meyer, P. / Leulliot, N. / Sorel, I. / Janin, J. / van Tilbeurgh, H. / Quevillon-Cheruel, S.
CitationJournal: Biochimie / Year: 2005
Title: Crystal structure of the S. cerevisiae D-ribose-5-phosphate isomerase: comparison with the archaeal and bacterial enzymes
Authors: Graille, M. / Meyer, P. / Leulliot, N. / Sorel, I. / Janin, J. / Van Tilbeurgh, H. / Quevillon-Cheruel, S.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose-5-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)29,1241
Polymers29,1241
Non-polymers00
Water2,396133
1
A: Ribose-5-phosphate isomerase

A: Ribose-5-phosphate isomerase

A: Ribose-5-phosphate isomerase

A: Ribose-5-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)116,4964
Polymers116,4964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Buried area9430 Å2
ΔGint-36 kcal/mol
Surface area37260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)209.240, 209.240, 209.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

21A-277-

HOH

31A-286-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer by the operations: Z, -Y, X; 1/2 -Z, -Y, 1/2-X; 1/2 -X, Y, 1/2-Z

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Components

#1: Protein Ribose-5-phosphate isomerase / Phosphoriboisomerase / D-ribose-5-phosphate ketol-isomerase


Mass: 29123.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RKI1 / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q12189, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Magnesium Chloride, 30% Polyethylene Glycol 4000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 3, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23476 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rsym value: 0.134 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.25 Å / Mean I/σ(I) obs: 6.4 / Rsym value: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LK5

1lk5


Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.775 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24733 1159 5 %RANDOM
Rwork0.1926 ---
obs0.19529 22023 100 %-
all-23182 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.368 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 0 133 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9482658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85124.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49715346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.1781511
X-RAY DIFFRACTIONr_chiral_restr0.1240.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2889
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21329
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1431.51262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8621961
X-RAY DIFFRACTIONr_scbond_it2.8433805
X-RAY DIFFRACTIONr_scangle_it4.1964.5697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 80 -
Rwork0.221 1536 -
obs--100 %

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