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- PDB-6ghw: Substituting the prolines of 4-oxalocrotonate tautomerase with no... -

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Basic information

Entry
Database: PDB / ID: 6ghw
TitleSubstituting the prolines of 4-oxalocrotonate tautomerase with non-canonical analogue (2S)-3,4-dehydroproline
Components2-hydroxymuconate tautomerase
KeywordsISOMERASE / non-canonical amino acid / (2S)-3 / 4-dehydroproline
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPavkov-Keller, T. / Lukesch, M.S. / Wiltschi, B. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund901 Austria
CitationJournal: Sci Rep / Year: 2019
Title: Substituting the catalytic proline of 4-oxalocrotonate tautomerase with non-canonical analogues reveals a finely tuned catalytic system.
Authors: Lukesch, M.S. / Pavkov-Keller, T. / Gruber, K. / Zangger, K. / Wiltschi, B.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)20,4944
Polymers20,4533
Non-polymers401
Water1,22568
1
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase

A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase

A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase


Theoretical massNumber of molelcules
Total (without water)40,9076
Polymers40,9076
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12950 Å2
ΔGint-92 kcal/mol
Surface area13290 Å2
MethodPISA
2
C: 2-hydroxymuconate tautomerase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)41,14712
Polymers40,9076
Non-polymers2406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12670 Å2
ΔGint-77 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.296, 85.296, 155.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-117-

HOH

21B-115-

HOH

31B-120-

HOH

41C-217-

HOH

51C-220-

HOH

61C-221-

HOH

71C-226-

HOH

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Components

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


Mass: 6817.809 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 (E. coli) / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 88% of 1-45 Morpheus condition (0.12M Alcohols, 0.1M Tris (base), BICINE pH 8.5, 50% v/v Precipitant mix composed of 40% v/v PEG 500 MME; 20 % w/v PEG 20000). protein concentration 6 mg/ml n ...Details: 88% of 1-45 Morpheus condition (0.12M Alcohols, 0.1M Tris (base), BICINE pH 8.5, 50% v/v Precipitant mix composed of 40% v/v PEG 500 MME; 20 % w/v PEG 20000). protein concentration 6 mg/ml n 0.1M PCTP buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→35.98 Å / Num. obs: 9550 / % possible obs: 96 % / Redundancy: 2.8 % / Biso Wilson estimate: 27.37 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.114 / Rrim(I) all: 0.199 / Net I/σ(I): 4.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.541 / Num. unique obs: 764 / CC1/2: 0.62 / Rpim(I) all: 0.405 / Rrim(I) all: 0.68 / % possible all: 78.26

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x19

4x19


Resolution: 2.3→35.934 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36
Details: Only 3 molecules could be build in the electron density. The fourth molecule can be seen but the density is interupted and not clearly defined (probably several conformations of this ...Details: Only 3 molecules could be build in the electron density. The fourth molecule can be seen but the density is interupted and not clearly defined (probably several conformations of this molecule - that with symmetry forms one of the hexamers). Therefore, we omitted the molecule 4 from the refinement. This also has a direct relation on higher Rfactors.
RfactorNum. reflection% reflection
Rfree0.3197 495 5.18 %
Rwork0.288 --
obs0.2897 9551 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 1 68 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011311
X-RAY DIFFRACTIONf_angle_d0.3381758
X-RAY DIFFRACTIONf_dihedral_angle_d1.899801
X-RAY DIFFRACTIONf_chiral_restr0.042213
X-RAY DIFFRACTIONf_plane_restr0.001228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.53130.38621100.31822061X-RAY DIFFRACTION89
2.5313-2.89740.32881190.29632313X-RAY DIFFRACTION99
2.8974-3.64990.31391320.28322310X-RAY DIFFRACTION99
3.6499-35.93840.30331340.27922372X-RAY DIFFRACTION97

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