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- PDB-1otf: 4-OXALOCROTONATE TAUTOMERASE-TRICLINIC CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1otf
Title4-OXALOCROTONATE TAUTOMERASE-TRICLINIC CRYSTAL FORM
Components4-OXALOCROTONATE TAUTOMERASE
KeywordsISOMERASE / TAUTOMERASE
Function / homology
Function and homology information


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
2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSubramanya, H.S. / Roper, D.I. / Dauter, Z. / Dodson, E.J. / Davies, G.J. / Wilson, K.S. / Wigley, D.B.
CitationJournal: Biochemistry / Year: 1996
Title: Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases.
Authors: Subramanya, H.S. / Roper, D.I. / Dauter, Z. / Dodson, E.J. / Davies, G.J. / Wilson, K.S. / Wigley, D.B.
History
DepositionNov 9, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)41,9046
Polymers41,9046
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-64 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 51.500, 51.600
Angle α, β, γ (deg.)60.00, 81.40, 69.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
4-OXALOCROTONATE TAUTOMERASE / 4-OXALOCROTONATE ISOMERASE


Mass: 6984.024 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CF600 / Description: T7 PROMOTER / Gene: DMPL / Plasmid: PET3A / Gene (production host): DMPL / Production host: Escherichia coli (E. coli)
References: UniProt: P49172, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1drop
21 %PEG2001drop
31 mMdithiothreitol1drop
43 Mammonium sulfate1drop
52.5-2.8 Mammonium sulfate1reservoir
610 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 6, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24515 / % possible obs: 93.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→10 Å /
RfactorNum. reflection
obs0.202 24401
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 0 149 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.492
X-RAY DIFFRACTIONp_mcangle_it2.332.5
X-RAY DIFFRACTIONp_scbond_it2.572
X-RAY DIFFRACTIONp_scangle_it4.182.5
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.0390.06
X-RAY DIFFRACTIONp_singtor_nbd0.1950.3
X-RAY DIFFRACTIONp_multtor_nbd0.2720.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1860.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.8215
X-RAY DIFFRACTIONp_staggered_tor20.3920
X-RAY DIFFRACTIONp_orthonormal_tor42.8320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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