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- PDB-1tqj: Crystal structure of D-ribulose 5-phosphate 3-epimerase from Syne... -

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Basic information

Entry
Database: PDB / ID: 1tqj
TitleCrystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 angstrom resolution
ComponentsRibulose-phosphate 3-epimerase
KeywordsISOMERASE / beta-alpha barrel epimerase
Function / homology
Function and homology information


ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose catabolic process / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
Ribulose-phosphate 3-epimerase / Ribulose-phosphate 3-epimerase family signature 2. / Ribulose-phosphate 3-epimerase family signature 1. / Ribulose-phosphate 3-epimerase-like / Ribulose-phosphate 3 epimerase family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribulose-phosphate 3-epimerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWise, E.L. / Akana, J. / Gerlt, J.A. / Rayment, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.
Authors: Wise, E.L. / Akana, J. / Gerlt, J.A. / Rayment, I.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose-phosphate 3-epimerase
B: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
E: Ribulose-phosphate 3-epimerase
F: Ribulose-phosphate 3-epimerase


Theoretical massNumber of molelcules
Total (without water)149,9876
Polymers149,9876
Non-polymers00
Water25,9241439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-86 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.564, 87.779, 97.821
Angle α, β, γ (deg.)90.00, 114.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribulose-phosphate 3-epimerase / Pentose-5-phosphate 3- epimerase / PPE / R5P3E


Mass: 24997.803 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: RPE, SLL0807 / Production host: Escherichia coli (E. coli) / References: UniProt: P74061, ribulose-phosphate 3-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1439 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6
Details: 22% methyl ether PEG 2000, 200 mM MgCl2, and 100 mM MES pH 6.0, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 156808 / Num. obs: 156808 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.336 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.826 / SU ML: 0.064 / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.101 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21962 7861 5 %5%
Rwork0.17016 ---
all0.17259 148947 --
obs0.17259 148947 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.6 Å2
2---0.39 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9869 0 0 1439 11308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210071
X-RAY DIFFRACTIONr_bond_other_d0.0020.029494
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.95913726
X-RAY DIFFRACTIONr_angle_other_deg1.264322054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85251279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.21619
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211128
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021841
X-RAY DIFFRACTIONr_nbd_refined0.2410.22196
X-RAY DIFFRACTIONr_nbd_other0.2460.211569
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.26086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2988
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6742.56479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.643410480
X-RAY DIFFRACTIONr_scbond_it3.64853592
X-RAY DIFFRACTIONr_scangle_it5.6016.53246
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 500
Rwork0.252 10043

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