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- PDB-9ll3: X-ray structure of Enterobacter cloaca transaldolase in complex w... -

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Basic information

Entry
Database: PDB / ID: 9ll3
TitleX-ray structure of Enterobacter cloaca transaldolase in complex with D-fructose-6-phosphate.
ComponentsFructose-6-phosphate aldolase
KeywordsTRANSFERASE / transaldolase
Function / homology
Function and homology information


ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / cytoplasm
Similarity search - Function
Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Fructose-6-phosphate aldolase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKamitori, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Synthetic Study of 8- and 9-Carbon Sugars by Transaldolase.
Authors: Yoshihara, A. / Miyoshi, E. / Tomino, S. / Hanaki, Y. / Mochizuki, S. / Yoshida, H. / Izumori, K. / Kamitori, S.
History
DepositionJan 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-6-phosphate aldolase
B: Fructose-6-phosphate aldolase
C: Fructose-6-phosphate aldolase
D: Fructose-6-phosphate aldolase
E: Fructose-6-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,95710
Polymers126,6565
Non-polymers1,3015
Water11,908661
1
A: Fructose-6-phosphate aldolase
B: Fructose-6-phosphate aldolase
C: Fructose-6-phosphate aldolase
D: Fructose-6-phosphate aldolase
E: Fructose-6-phosphate aldolase
hetero molecules

A: Fructose-6-phosphate aldolase
B: Fructose-6-phosphate aldolase
C: Fructose-6-phosphate aldolase
D: Fructose-6-phosphate aldolase
E: Fructose-6-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,91320
Polymers253,31210
Non-polymers2,60110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area44890 Å2
ΔGint-331 kcal/mol
Surface area69490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.560, 179.960, 133.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-434-

HOH

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Components

#1: Protein
Fructose-6-phosphate aldolase


Mass: 25331.182 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: fsa, DP202_18755 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A330G8J7, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-F6R / FRUCTOSE -6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM cacodylate buffer, pH 6.5, 10% (w/v) PEG3000, 10% (w/v) PEG 8000, 200 mM of MgCl2, 20 mM dihydroxtacetone, 20 mM, 20 mM D,L-glyceraldehyde-3-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→19.6 Å / Num. obs: 90439 / % possible obs: 99.8 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.7
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6596 / CC1/2: 0.771

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S1V

3s1v


Resolution: 1.92→19.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.816 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20128 4537 5 %RANDOM
Rwork0.16583 ---
obs0.16762 85902 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.293 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.92→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 0 661 8831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0128290
X-RAY DIFFRACTIONr_bond_other_d00.0168275
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.80411295
X-RAY DIFFRACTIONr_angle_other_deg0.4351.72719045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65251095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.557535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61101375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029545
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6611.7494395
X-RAY DIFFRACTIONr_mcbond_other1.6591.7494395
X-RAY DIFFRACTIONr_mcangle_it2.2723.1375485
X-RAY DIFFRACTIONr_mcangle_other2.2733.1385486
X-RAY DIFFRACTIONr_scbond_it3.42.1833895
X-RAY DIFFRACTIONr_scbond_other3.3872.1773892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0393.8495811
X-RAY DIFFRACTIONr_long_range_B_refined6.28218.659211
X-RAY DIFFRACTIONr_long_range_B_other6.25417.929028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 352 -
Rwork0.228 6246 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1653-0.1069-0.02630.21510.00670.0087-0.00860.0034-0.013-0.01350.01370.02460.01010-0.00520.0204-0.0049-0.01030.018-0.0020.0088-13.73-60.544116.7519
20.13070.0591-0.01050.2270.00390.00290.0057-0.0063-0.0049-0.0328-0.0002-0.0320.00080.0013-0.00550.02330.00010.0060.0066-0.00360.011420.5908-56.415617.9126
30.219-0.1673-0.01090.29230.03620.00680.0420.02580.0307-0.0227-0.0305-0.0496-0.0036-0.0068-0.01150.01730.01180.01510.01610.01320.023127.1812-22.435618.0629
40.204-0.06990.05120.13080.01210.02280.01040.00030.0181-0.0372-0.0029-0.0246-0.0076-0.0057-0.00750.01420.00570.01220.01950.01360.0154-2.9938-5.345217.2591
50.06080.03720.00510.3008-0.02450.02970.0160.01520.0016-0.00610.00240.03830.0073-0.0113-0.01840.00590.003-0.00420.02260.0070.0134-28.317-29.010216.2724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 220
4X-RAY DIFFRACTION4D1 - 220
5X-RAY DIFFRACTION5E1 - 220

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