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- PDB-3ctl: Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Esch... -

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Basic information

Entry
Database: PDB / ID: 3ctl
TitleCrystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12 complexed with D-glucitol 6-phosphate and magnesium
ComponentsD-allulose-6-phosphate 3-epimerase
KeywordsISOMERASE / D-Allulose 6-Phosphate 3-Epimerase / D-glucitol 6-phosphate / (beta/alpha)8 barrel / Carbohydrate metabolism
Function / homology
Function and homology information


allulose 6-phosphate 3-epimerase activity / D-allose catabolic process / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / D-ribulose-phosphate 3-epimerase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
D-allulose-6-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
D-SORBITOL-6-PHOSPHATE / D-allulose-6-phosphate 3-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.
Authors: Chan, K.K. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: D-allulose-6-phosphate 3-epimerase
B: D-allulose-6-phosphate 3-epimerase
C: D-allulose-6-phosphate 3-epimerase
D: D-allulose-6-phosphate 3-epimerase
E: D-allulose-6-phosphate 3-epimerase
F: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,56618
Polymers156,8476
Non-polymers1,71912
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-141.3 kcal/mol
Surface area44320 Å2
MethodPISA
2
D: D-allulose-6-phosphate 3-epimerase
F: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.8 kcal/mol
Surface area17070 Å2
MethodPISA
3
B: D-allulose-6-phosphate 3-epimerase
E: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.6 kcal/mol
Surface area17160 Å2
MethodPISA
4
A: D-allulose-6-phosphate 3-epimerase
C: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.5 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.706, 129.040, 154.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
D-allulose-6-phosphate 3-epimerase


Mass: 26141.189 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alsE, yjcU / Production host: Escherichia coli (E. coli)
References: UniProt: P32719, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Sugar
ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.1 M Succinic acid, pH 7.0, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 74982 / Num. obs: 74982 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CT7

3ct7


Resolution: 2.2→24.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1665519.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3777 5 %RANDOM
Rwork0.243 ---
obs0.243 74982 96.5 %-
all-74982 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9587 Å2 / ksol: 0.348849 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.5 Å20 Å20 Å2
2---6.69 Å20 Å2
3----0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10464 0 102 174 10740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.386 353 5 %
Rwork0.379 6689 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GPH_par.txtGPH_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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