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- PDB-4otc: 4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, TRIGONAL... -

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Basic information

Entry
Database: PDB / ID: 4otc
Title4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, TRIGONAL CRYSTAL FORM
Components4-OXALOCROTONATE TAUTOMERASE
KeywordsISOMERASE / TAUTOMERASE / MICROBIAL BIODEGRADATION
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
2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsTaylor, A.B. / Whitman, C.P. / Hackert, M.L.
Citation
Journal: Thesis / Year: 1998
Title: Native and inhibitor complex structures of 4-oxalocrotonate tautomerase from Pseudomonas putida mt-2 (University of Texas at Austin-136 pages)
Authors: Taylor, A.B.
#1: Journal: Biochemistry / Year: 1998
Title: Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis
Authors: Taylor, A.B. / Czerwinski, R.M. / Johnson Jr., W.H. / Whitman, C.P. / Hackert, M.L.
History
DepositionOct 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,12627
Polymers61,3979
Non-polymers1,72918
Water1,08160
1
A: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)42,08418
Polymers40,9316
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
2
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0286
Polymers13,6442
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15590 Å2
ΔGint-280 kcal/mol
Surface area13740 Å2
MethodPISA
3
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0286
Polymers13,6442
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-287 kcal/mol
Surface area13620 Å2
MethodPISA
4
F: 4-OXALOCROTONATE TAUTOMERASE
G: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0286
Polymers13,6442
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15710 Å2
ΔGint-293 kcal/mol
Surface area13680 Å2
MethodPISA
5
H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,08418
Polymers40,9316
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15650 Å2
ΔGint-281 kcal/mol
Surface area13710 Å2
MethodPISA, PQS
6
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,08418
Polymers40,9316
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
7
F: 4-OXALOCROTONATE TAUTOMERASE
G: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

F: 4-OXALOCROTONATE TAUTOMERASE
G: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

F: 4-OXALOCROTONATE TAUTOMERASE
G: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,08418
Polymers40,9316
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
8
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,08418
Polymers40,9316
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.000, 88.000, 124.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999882, 0.013432, -0.007496), (-0.013436, 0.99991, -0.000567), (0.007487, 0.000668, 0.999972)0.5559, 50.82938, -36.62017
2given(0.999307, -0.030735, 0.020986), (-0.031097, -0.999369, 0.017163), (0.020445, -0.017803, -0.999632)-1.36861, 49.59311, 88.15522
3given(0.918094, -0.396051, 0.015724), (0.396202, 0.91813, -0.007888), (-0.011313, 0.013472, 0.999845)-1.00247, 51.30989, 48.98172
4given(0.921005, 0.389206, -0.016351), (0.389131, -0.92115, -0.007692), (-0.018055, 0.000722, -0.999837)1.16117, 51.38737, 173.60204
5given(0.877341, -0.479824, -0.006506), (-0.479815, -0.877365, 0.00302), (-0.007157, 0.000472, -0.999974)0.48691, 50.57769, 126.34159
6given(0.876987, 0.480239, -0.016265), (-0.480139, 0.877137, 0.009846), (0.018995, -0.000825, 0.999819)1.12491, 50.0617, 1.90041
7given(0.875081, -0.483866, -0.010354), (0.483842, 0.875142, -0.004904), (0.011434, -0.000718, 0.999934)0.77616, 0.31906, -38.33271
8given(0.876074, 0.482066, -0.010353), (0.482047, -0.876134, -0.00439), (-0.011187, -0.001145, -0.999937)0.79011, 0.31814, 86.17117

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Components

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


Mass: 6821.838 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: MT-2 / Plasmid: PBAOT1 / Gene (production host): XYLH / Production host: Escherichia coli (E. coli) / Strain (production host): S606
References: UniProt: Q01468, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→20 Å / Num. obs: 24989 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.047 / Net I/σ(I): 12.1
Reflection shellResolution: 2.28→2.46 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.114 / % possible all: 79.7

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTF

1otf


Resolution: 2.28→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2416 9.7 %RANDOM
Rwork0.234 ---
obs0.234 24917 95.8 %-
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-20 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 90 60 4245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.28→2.36 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.322 136 8.8 %
Rwork0.282 1402 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION3SO4.PARSO4.TOP

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