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- PDB-9hzi: X-ray Crystallographic Structure of 4-OT (F11) in complex with 2-... -

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Basic information

Entry
Database: PDB / ID: 9hzi
TitleX-ray Crystallographic Structure of 4-OT (F11) in complex with 2-Hydroxycinnamaldehyde
Components2-hydroxymuconate tautomerase
KeywordsLYASE / Asymmetric trimer / Proline catalysis / Michael Addition Reactions
Function / homology
Function and homology information


xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily
Similarity search - Domain/homology
: / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsRohan, S. / Tittmann, K. / Rabe von Pappenheim, F. / Poelarends, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)101073065European Union
CitationJournal: To Be Published
Title: X-Ray Crystallographic Structure of 4-OT (F11) in complex with 2-Hydroxycinnamaldehyde
Authors: Rohan, S. / Tittmann, K. / Rabe von Pappenheim, F. / Poelarends, G.
History
DepositionJan 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7486
Polymers41,0573
Non-polymers6913
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-30 kcal/mol
Surface area15210 Å2
Unit cell
Length a, b, c (Å)38.685, 49.888, 87.022
Angle α, β, γ (deg.)90.000, 97.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 2-hydroxymuconate tautomerase / 4-oxalocrotonate tautomerase / 4-OT


Mass: 13685.563 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Chemical ChemComp-A1IZH / (1~{Z},2~{S})-1-[(~{E})-3-(2-hydroxyphenyl)prop-2-enylidene]-1$l^{4}-azolidine-2-carbaldehyde


Mass: 230.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H16NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Reservoir Volume = 500 microliter Reservoir Composition PEG 2000 (15%) Urea (13 mM) Bis-Tris pH 7.0 (0.1 M) Drop Preparation 2-Hydroxycinnamaldehyde was saturated in 5mM KH2PO4 pH 7.3. 4-OT ...Details: Reservoir Volume = 500 microliter Reservoir Composition PEG 2000 (15%) Urea (13 mM) Bis-Tris pH 7.0 (0.1 M) Drop Preparation 2-Hydroxycinnamaldehyde was saturated in 5mM KH2PO4 pH 7.3. 4-OT (F11) was diluted from the storage stock (104.6 mg/mL) to the working stock (16mg/mL) using the above saturated solution. Drop Volume= 1microliter protein solution (protein in 5mM KH2PO4 pH 7.3 (16 mg/ml) + 1microliter precipitant solution Drop Composition PEG 2000 (7.5%) Urea (6.5 mM) Bis-Tris pH 7.0 (0.05 M) Guanidine Hydrochloride (0.08 M)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976256 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Apr 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 2.267→33.357 Å / Num. obs: 13467 / % possible obs: 87.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 41.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.9
Reflection shellResolution: 2.267→2.306 Å / Num. unique obs: 670 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoXDS1.1.7 (20210504)data reduction
XDSVERSION Jun 30, 2023 BUILT= 20230630data reduction
autoXDS1.1.7 (20210504)data scaling
Aimless0.7.7data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→33.357 Å / SU ML: 0.3615 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 636 4.73 %
Rwork0.2183 12819 -
obs0.2209 13455 87.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.44 Å2
Refinement stepCycle: LAST / Resolution: 2.27→33.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 51 63 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022906
X-RAY DIFFRACTIONf_angle_d0.41853906
X-RAY DIFFRACTIONf_chiral_restr0.046456
X-RAY DIFFRACTIONf_plane_restr0.0035507
X-RAY DIFFRACTIONf_dihedral_angle_d11.90681111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.440.37171550.28232731X-RAY DIFFRACTION94.25
2.44-2.60.353920.27921951X-RAY DIFFRACTION96.23
2.72-3.080.31831400.24512479X-RAY DIFFRACTION96.57
3.08-3.870.28531050.22342753X-RAY DIFFRACTION91.99
3.88-33.3570.22621440.18882905X-RAY DIFFRACTION96.58
Refinement TLS params.Method: refined / Origin x: 1.25918016478 Å / Origin y: 14.3367800327 Å / Origin z: 22.2610611993 Å
111213212223313233
T0.237969556203 Å20.0198331706187 Å20.00409492020614 Å2-0.247978994702 Å2-0.00653745539008 Å2--0.265615465608 Å2
L2.56589986451 °2-0.303437952317 °20.347318906102 °2-1.68330216393 °2-0.197278457046 °2--1.65705651731 °2
S-0.0192002442238 Å °-0.0774206046636 Å °0.111529943777 Å °0.056786396437 Å °-0.0429084154787 Å °-0.144705668614 Å °-0.0389883443539 Å °-0.115797667574 Å °0.0519505689704 Å °
Refinement TLS groupSelection details: all

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