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- PDB-6bgn: Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubatio... -

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Basic information

Entry
Database: PDB / ID: 6bgn
TitleCrystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate
Components2-hydroxymuconate tautomerase
KeywordsISOMERASE
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 / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-fluoranyl-2-oxidanylidene-pentanoic acid / NITRATE ION / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.51 Å
AuthorsZhang, Y. / Li, W. / Stack, T.
CitationJournal: Biochemistry / Year: 2018
Title: Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates.
Authors: Stack, T.M.M. / Li, W. / Johnson, W.H. / Zhang, Y.J. / Whitman, C.P.
History
DepositionOct 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
D: 2-hydroxymuconate tautomerase
E: 2-hydroxymuconate tautomerase
F: 2-hydroxymuconate tautomerase
G: 2-hydroxymuconate tautomerase
H: 2-hydroxymuconate tautomerase
I: 2-hydroxymuconate tautomerase
J: 2-hydroxymuconate tautomerase
K: 2-hydroxymuconate tautomerase
L: 2-hydroxymuconate tautomerase
M: 2-hydroxymuconate tautomerase
N: 2-hydroxymuconate tautomerase
O: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,46751
Polymers97,61215
Non-polymers3,85536
Water11,476637
1
A: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6422
Polymers6,5071
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9185
Polymers6,5071
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6422
Polymers6,5071
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8264
Polymers6,5071
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8885
Polymers6,5071
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8885
Polymers6,5071
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7964
Polymers6,5071
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7343
Polymers6,5071
Non-polymers2262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.413, 88.011, 112.674
Angle α, β, γ (deg.)90.000, 98.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11K-227-

HOH

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Components

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


Mass: 6507.450 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Chemical
ChemComp-6Y5 / 5-fluoranyl-2-oxidanylidene-pentanoic acid


Mass: 134.106 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C5H7FO3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, pH 6.5, with 20% PEG 4600 (w/v), and 0.1 M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 131636 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 32.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.51→43.29 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.509 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1694 6595 5 %RANDOM
Rwork0.1156 ---
obs0.1183 124537 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 214.76 Å2 / Biso mean: 22.54 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.78 Å2
2---0.64 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.51→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6735 0 255 641 7631
Biso mean--39.58 33.52 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197345
X-RAY DIFFRACTIONr_bond_other_d0.0010.027439
X-RAY DIFFRACTIONr_angle_refined_deg1.2692.0039839
X-RAY DIFFRACTIONr_angle_other_deg0.709317224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91223.742302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.547151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6641572
X-RAY DIFFRACTIONr_chiral_restr0.0750.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028025
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021451
X-RAY DIFFRACTIONr_mcbond_it6.2511.8243632
X-RAY DIFFRACTIONr_mcbond_other6.1781.8223631
X-RAY DIFFRACTIONr_mcangle_it7.7952.724538
X-RAY DIFFRACTIONr_rigid_bond_restr6.441314784
X-RAY DIFFRACTIONr_sphericity_free41.135152
X-RAY DIFFRACTIONr_sphericity_bonded23.407515191
LS refinement shellResolution: 1.511→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 456 -
Rwork0.122 8849 -
all-9305 -
obs--95.79 %

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