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- PDB-9ftk: Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase... -

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Basic information

Entry
Database: PDB / ID: 9ftk
TitleCrystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3 bound to substrate intermediate
ComponentsTrans-O-hydroxybenzylidenepyruvate hydratase-aldolase
KeywordsLYASE / hydratase / aldolase
Function / homology
Function and homology information


trans-o-hydroxybenzylidenepyruvate hydratase-aldolase / naphthalene catabolic process / aldehyde-lyase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
: / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
(4R)-4-hydroxy-4-(2-hydroxyphenyl)butanoic acid / SALICYLALDEHYDE / PHOSPHATE ION / Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMilani, M. / Ferrara, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural snapshots of the aldol condensation reaction of the enzyme trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3.
Authors: Ferrara, S. / Braggiotti, B. / Mastrangelo, E. / Di Gennaro, P. / Bertoni, G. / Milani, M.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
C: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
D: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
G: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
H: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
J: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
K: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,35053
Polymers307,1028
Non-polymers5,24845
Water71,0693945
1
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
C: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
D: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,23427
Polymers153,5514
Non-polymers2,68323
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-158 kcal/mol
Surface area40150 Å2
2
G: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
H: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
J: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
K: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,11526
Polymers153,5514
Non-polymers2,56422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-158 kcal/mol
Surface area40110 Å2
Unit cell
Length a, b, c (Å)144.511, 199.715, 144.511
Angle α, β, γ (deg.)90.000, 92.581, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 8 molecules ABCDGHJK

#1: Protein
Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase / 2'-hydroxybenzalpyruvate aldolase


Mass: 38387.730 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nahE / Production host: Escherichia coli (E. coli)
References: UniProt: C3KFM9, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase

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Non-polymers , 5 types, 3990 molecules

#2: Chemical
ChemComp-KRN / (4R)-4-hydroxy-4-(2-hydroxyphenyl)butanoic acid


Mass: 196.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H12O4
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NK / SALICYLALDEHYDE


Mass: 122.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3945 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.76→46.7 Å / Num. obs: 366454 / % possible obs: 90.5 % / Redundancy: 2 % / CC1/2: 0.994 / Rrim(I) all: 0.107 / Net I/σ(I): 6.2
Reflection shellResolution: 1.76→1.85 Å / Redundancy: 2 % / Num. unique obs: 53349 / CC1/2: 0.819 / Rrim(I) all: 0.61 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→46.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2154 18623 5.084 %
Rwork0.1773 347687 -
all0.179 --
obs-366310 90.464 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å20.136 Å2
2--0.335 Å20 Å2
3----0.344 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20262 0 334 3945 24541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01221375
X-RAY DIFFRACTIONr_bond_other_d0.0020.01620008
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.82329106
X-RAY DIFFRACTIONr_angle_other_deg1.0681.76546104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45252686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.2115186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84103432
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.210917
X-RAY DIFFRACTIONr_chiral_restr0.090.23197
X-RAY DIFFRACTIONr_chiral_restr_other0.9530.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225546
X-RAY DIFFRACTIONr_gen_planes_other0.0110.024974
X-RAY DIFFRACTIONr_nbd_refined0.2310.24913
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.219413
X-RAY DIFFRACTIONr_nbtor_refined0.1840.210725
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.210355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.23221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2480.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3410.255
X-RAY DIFFRACTIONr_nbd_other0.1780.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2830.25
X-RAY DIFFRACTIONr_mcbond_it1.3471.48310522
X-RAY DIFFRACTIONr_mcbond_other1.3461.48310522
X-RAY DIFFRACTIONr_mcangle_it2.0382.65613162
X-RAY DIFFRACTIONr_mcangle_other2.0392.65713163
X-RAY DIFFRACTIONr_scbond_it2.5881.82110853
X-RAY DIFFRACTIONr_scbond_other2.5881.82110853
X-RAY DIFFRACTIONr_scangle_it4.0173.19615904
X-RAY DIFFRACTIONr_scangle_other4.0173.19615905
X-RAY DIFFRACTIONr_lrange_it6.31618.58127216
X-RAY DIFFRACTIONr_lrange_other6.318.17626968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8030.41613180.38724759X-RAY DIFFRACTION86.9755
1.803-1.8520.35514500.3425709X-RAY DIFFRACTION93.4777
1.852-1.9050.29213640.28325012X-RAY DIFFRACTION93.2377
1.905-1.9640.27813020.25324259X-RAY DIFFRACTION93.132
1.964-2.0280.24913140.22123482X-RAY DIFFRACTION92.8689
2.028-2.0990.2412560.222610X-RAY DIFFRACTION92.6259
2.099-2.1780.22912120.1921789X-RAY DIFFRACTION92.3624
2.178-2.2670.20310350.16821056X-RAY DIFFRACTION92.0382
2.267-2.3680.19610810.15319934X-RAY DIFFRACTION91.5686
2.368-2.4830.1859800.1419056X-RAY DIFFRACTION91.276
2.483-2.6170.1849740.13717994X-RAY DIFFRACTION90.6346
2.617-2.7750.1738630.1317002X-RAY DIFFRACTION90.118
2.775-2.9660.1848610.13315755X-RAY DIFFRACTION89.4873
2.966-3.2030.188020.13814601X-RAY DIFFRACTION88.7474
3.203-3.5070.1856900.14813272X-RAY DIFFRACTION87.5965
3.507-3.9180.1916110.14911939X-RAY DIFFRACTION86.6653
3.918-4.5190.1725650.13610272X-RAY DIFFRACTION85.0027
4.519-5.5210.1844360.1528691X-RAY DIFFRACTION84.5171
5.521-7.7550.1993100.1776766X-RAY DIFFRACTION84.218
7.755-46.70.2251990.1733729X-RAY DIFFRACTION81.6123

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