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- PDB-9lkp: X-ray structure of Enterobacter cloaca transaldolase -

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Basic information

Entry
Database: PDB / ID: 9lkp
TitleX-ray structure of Enterobacter cloaca transaldolase
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 aldolase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 16, 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


Theoretical massNumber of molelcules
Total (without water)126,6565
Polymers126,6565
Non-polymers00
Water14,952830
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

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


Theoretical massNumber of molelcules
Total (without water)253,31210
Polymers253,31210
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area39680 Å2
ΔGint-300 kcal/mol
Surface area70700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.000, 180.070, 134.040
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-334-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.84 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→46.68 Å / Num. obs: 148396 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.6
Reflection shellResolution: 1.63→1.67 Å / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10888 / CC1/2: 0.736

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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: 1.63→46.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.359 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19735 7448 5 %RANDOM
Rwork0.17331 ---
obs0.17451 140948 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--0.12 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.63→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8095 0 0 830 8925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128215
X-RAY DIFFRACTIONr_bond_other_d00.0168255
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.80111185
X-RAY DIFFRACTIONr_angle_other_deg0.4381.7318980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24151095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.728535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.537101375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029525
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_it1.6241.654395
X-RAY DIFFRACTIONr_mcbond_other1.6241.654395
X-RAY DIFFRACTIONr_mcangle_it2.1612.9585485
X-RAY DIFFRACTIONr_mcangle_other2.1622.9585486
X-RAY DIFFRACTIONr_scbond_it3.3332.0153820
X-RAY DIFFRACTIONr_scbond_other3.3332.0153821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8093.5295701
X-RAY DIFFRACTIONr_long_range_B_refined5.48217.349173
X-RAY DIFFRACTIONr_long_range_B_other5.44616.278956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 518 -
Rwork0.248 10360 -
obs--99.89 %
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)
10.12890.0803-0.02460.2092-0.00610.0074-0.01560.0081-0.00880.0290.0195-0.0390.0074-0.0058-0.00390.03120.0046-0.01220.01740.00080.010713.8199-60.4471-16.8823
20.1473-0.058-0.00510.2508-0.00350.00130.0055-0.0002-0.00320.0333-0.0020.04850.00250.0028-0.00340.03840.00310.01040.01020.00210.0104-20.5713-56.3409-17.922
30.27480.2299-0.0320.3635-0.04130.01060.0537-0.01930.04080.0523-0.03460.0773-0.01040.0122-0.01910.0271-0.01090.0220.0161-0.01750.0303-27.116-22.4344-17.9648
40.16390.04940.04450.1618-0.01760.01920.00220.01070.01320.04520.00140.0244-0.00680.0057-0.00360.030900.01070.0176-0.00650.00813.0928-5.3062-17.3082
50.0663-0.03470.01460.34970.01320.02420.0094-0.0087-0.0020.01670.0076-0.05250.0062-0.0042-0.0170.01260.0005-0.00750.0136-0.00320.018128.4387-28.9722-16.4438
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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