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- PDB-4ota: 4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, ORTHORHO... -

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Basic information

Entry
Database: PDB / ID: 4ota
Title4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, ORTHORHOMBIC 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: 2.75 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: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
J: 4-OXALOCROTONATE TAUTOMERASE
K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE
M: 4-OXALOCROTONATE TAUTOMERASE
N: 4-OXALOCROTONATE TAUTOMERASE
O: 4-OXALOCROTONATE TAUTOMERASE
P: 4-OXALOCROTONATE TAUTOMERASE
Q: 4-OXALOCROTONATE TAUTOMERASE
R: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,29144
Polymers122,79318
Non-polymers2,49826
Water45025
1
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
F: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,89216
Polymers40,9316
Non-polymers96110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-255 kcal/mol
Surface area13960 Å2
MethodPISA
2
G: 4-OXALOCROTONATE TAUTOMERASE
H: 4-OXALOCROTONATE TAUTOMERASE
I: 4-OXALOCROTONATE TAUTOMERASE
J: 4-OXALOCROTONATE TAUTOMERASE
K: 4-OXALOCROTONATE TAUTOMERASE
L: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70014
Polymers40,9316
Non-polymers7698
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-215 kcal/mol
Surface area14010 Å2
MethodPISA
3
M: 4-OXALOCROTONATE TAUTOMERASE
N: 4-OXALOCROTONATE TAUTOMERASE
O: 4-OXALOCROTONATE TAUTOMERASE
P: 4-OXALOCROTONATE TAUTOMERASE
Q: 4-OXALOCROTONATE TAUTOMERASE
R: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70014
Polymers40,9316
Non-polymers7698
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-219 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.300, 98.200, 118.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.755949, -0.653504, -0.038391), (-0.652212, 0.746822, 0.129911), (-0.056226, 0.123245, -0.990782)-1.42363, -2.65529, 32.45121
2given(-0.488012, 0.869592, 0.075199), (-0.872716, -0.484694, -0.058642), (-0.014547, -0.094245, 0.995443)9.07884, -10.23798, -0.78759
3given(-0.19126, 0.980254, 0.050224), (0.981423, 0.191775, -0.0056), (-0.015121, 0.04822, -0.998722)10.01406, -8.86748, 31.7916
4given(-0.512583, -0.858609, -0.007054), (0.856087, -0.51041, -0.081215), (0.066131, -0.047668, 0.996672)-4.3607, -13.16601, -0.49364
5given(0.941552, -0.324959, -0.08878), (-0.327586, -0.944679, -0.016413), (-0.078534, 0.044537, -0.995916)-1.26025, -15.75716, 31.92196
6given(0.315175, -0.947421, -0.0553), (0.938904, 0.319772, -0.127298), (0.138288, -0.0118, 0.990322)-3.92153, -11.01508, 77.85254
7given(0.398431, -0.91373, -0.079692), (-0.911034, -0.404313, 0.080925), (-0.106164, 0.040359, -0.993529)-3.2693, -16.49777, 110.01126
8given(0.67562, 0.736687, 0.028798), (-0.737247, 0.674993, 0.029169), (0.00205, -0.040938, 0.999159)8.32856, -6.40743, 78.02151
9given(-0.993419, 0.114536, -0.001129), (0.113349, 0.984452, 0.134187), (0.016481, 0.133176, -0.990955)6.74743, -7.48451, 110.46095
10given(-0.973644, 0.217663, 0.068118), (-0.225484, -0.96353, -0.144109), (0.034266, -0.15567, 0.987214)6.62668, -19.19378, 76.86263
11given(0.605794, 0.79559, -0.007176), (0.795219, -0.605175, 0.037293), (0.025328, -0.028298, -0.999279)9.74666, -20.8298, 109.35571
12given(-0.106433, -0.993937, -0.02758), (0.986571, -0.102107, -0.127487), (0.123898, -0.040779, 0.991457)-4.70592, -11.45433, 38.61424
13given(0.740462, -0.662367, -0.113957), (-0.660818, -0.748427, 0.056361), (-0.12262, 0.033572, -0.991886)-2.3079, -16.33574, 70.78499
14given(0.913482, 0.406054, 0.025909), (-0.406234, 0.913767, 0.001876), (-0.022913, -0.012239, 0.999663)4.46594, -1.94487, 39.07974
15given(-0.959495, -0.280998, -0.020264), (-0.280327, 0.945086, 0.168014), (-0.02806, 0.166889, -0.985576)2.89366, -4.31044, 71.50256
16given(-0.802873, 0.589358, 0.089732), (-0.59615, -0.793574, -0.121842), (-0.0006, -0.151317, 0.988485)8.32751, -14.53264, 37.96559
17given(0.22005, 0.97531, 0.018667), (0.975427, -0.22021, 0.007026), (0.010963, 0.016662, -0.999801)10.77146, -14.67557, 70.51482

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Components

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


Mass: 6821.838 Da / Num. of mol.: 18
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


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 46 %
Description: PDB ENTRY 1OTF WAS USED TO SOLVE THE STARTING MOLECULAR REPLACEMENT MODEL
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 29560 / % possible obs: 98.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.134 / Net I/σ(I): 9.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.436 / % possible all: 97.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.3 ANGSTROMS RESOLUTION STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE FROM PSEUDOMONAS PUTIDA MT-2

Resolution: 2.75→25 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
Rfree0.266 2847 9.8 %RANDOM
Rwork0.228 ---
obs0.228 28918 96 %-
Displacement parametersBiso mean: 32.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-25 Å
Luzzati sigma a0.42 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8229 0 130 25 8384
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_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
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: 2.75→2.85 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.332 268 9.6 %
Rwork0.312 2522 -
obs--93.8 %
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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