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- PDB-1rpx: D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM SOLANUM TUBEROSUM CHLOROPLASTS -

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Basic information

Entry
Database: PDB / ID: 1rpx
TitleD-RIBULOSE-5-PHOSPHATE 3-EPIMERASE FROM SOLANUM TUBEROSUM CHLOROPLASTS
ComponentsPROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
Keywords3-EPIMERASE / CHLOROPLAST / CALVIN CYCLE / 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 / reductive pentose-phosphate cycle / chloroplast thylakoid membrane / 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, chloroplastic
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsKopp, J. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts.
Authors: Kopp, J. / Kopriva, S. / Suss, K.H. / Schulz, G.E.
History
DepositionDec 1, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
B: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
C: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2216
Polymers73,9333
Non-polymers2883
Water3,189177
1
A: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
B: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
C: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
hetero molecules

A: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
B: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
C: PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,44312
Polymers147,8666
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16120 Å2
ΔGint-168 kcal/mol
Surface area46020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.100, 146.100, 93.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.615618, -0.566417, -0.547872), (-0.721915, -0.126974, -0.680103), (0.315683, 0.814298, -0.487112)43.953, 85.756, -55.409
2given(0.615585, -0.722198, 0.315398), (-0.567238, -0.128436, 0.813339), (-0.546941, -0.679684, -0.488774)52.487, 80.938, 55.373

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Components

#1: Protein PROTEIN (RIBULOSE-PHOSPHATE 3-EPIMERASE)


Mass: 24644.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Organelle: CHLOROPLAST / Production host: Escherichia coli (E. coli) / References: UniProt: Q43843, ribulose-phosphate 3-epimerase
#2: Chemical ChemComp-SO4 / SULFATE ION


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

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.5 Mammonium sulfate1drop
310 mM1dropNaCl
410 mMMOPS/NaOH1drop
51 mMEDTA1drop
61 mM1dropNaN3
72.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 49783 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 33.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.206 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 265449 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
Agrovatadata reduction
X-PLOR3.8.5.1refinement
XDSdata reduction
CCP4(AGROVATAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→35 Å / Rfactor Rfree error: 0.0055 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: STANDARD BULK SOLVENT CORRECTION OF X-PLOR 3.851 USED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1500 3.01 %RANDOM
Rwork0.174 ---
obs-49783 97.2 %-
Displacement parametersBiso mean: 35 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 15 177 5388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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