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- PDB-1h1y: The structure of the cytosolic D-ribulose-5-phosphate 3-epimerase... -

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Basic information

Entry
Database: PDB / ID: 1h1y
TitleThe structure of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice complexed with sulfate
ComponentsD-RIBULOSE-5-PHOSPHATE 3-EPIMERASE
KeywordsISOMERASE / 3-EPIMERASE / OXIDATIVE PENTOSE PHOSPHATE PATHWAY
Function / homology
Function and homology information


ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / 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, cytoplasmic isoform
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJelakovic, S. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure and Catalytic Mechanism of the Cytosolic D-Ribulose-5-Phosphate 3-Epimerase from Rice
Authors: Jelakovic, S. / Kopriva, S. / Suss, K. / Schulz, G.E.
History
DepositionJul 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE
B: D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8264
Polymers48,6342
Non-polymers1922
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.280, 73.300, 88.970
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.894186, 0.163495, 0.416775), (0.157034, -0.986326, 0.050007), (0.419252, 0.020732, -0.907633)
Vector: -7.909, -2.429, 34.758)

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Components

#1: Protein D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE


Mass: 24316.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9SE42, ribulose-phosphate 3-epimerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES INTERCONVERSION BETWEEN D-RIBULOSE 5-PHOSPHATE AND D-XYLULOSE 5-PHOSPHATE. COMPONENT OF ...CATALYSES INTERCONVERSION BETWEEN D-RIBULOSE 5-PHOSPHATE AND D-XYLULOSE 5-PHOSPHATE. COMPONENT OF CALVIN CYCLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
21.0 Mammonium sulfate1drop
350 mMMOPS1droppH7.5
41 %(w/v)PEG4001drop
510 mMglycerol-3-phosphate1drop
65 mML-arginine1drop
72.0 Mammonium sulfate1reservoir
8100 mMMOPS1reservoirpH7.5
92 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.91
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.87→29 Å / Num. obs: 42044 / % possible obs: 98 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.021
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 29 Å / % possible obs: 98 %
Reflection shell
*PLUS
% possible obs: 98 % / Redundancy: 4.3 % / Num. unique obs: 5730 / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 16

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 --RANDOM
Rwork0.175 ---
obs0.175 42694 98.4 %-
Refinement stepCycle: LAST / Resolution: 1.87→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 10 467 3759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 29 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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