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- PDB-7fjk: Tyrosine phenol-lyase from pantoea agglomerans -

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Basic information

Entry
Database: PDB / ID: 7fjk
TitleTyrosine phenol-lyase from pantoea agglomerans
ComponentsTyrosine phenol-lyase
KeywordsLYASE / Tyrosine / Pyridoxal 5'-phosphate / Phenol
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process / cytoplasm
Similarity search - Function
Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesEnterobacter agglomerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKatayama, T. / Mikamii, B. / Byun, Z.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)20ak0101127h002 Japan
CitationJournal: To Be Published
Title: Faecal microbiota-dependent phenol production from tyrosine
Authors: Oikawa, D. / Byun, Z. / Gotoh, A. / Katoh, T. / Suzuki, C. / Kikuchi, K. / Mikami, B. / Katayama, T. / Nakayama, T. / Abe, T.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
C: Tyrosine phenol-lyase
D: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,66769
Polymers205,7194
Non-polymers4,94965
Water36,7872042
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33320 Å2
ΔGint115 kcal/mol
Surface area56100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.516, 161.077, 100.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-994-

HOH

21B-645-

HOH

31B-707-

HOH

41B-1002-

HOH

51B-1029-

HOH

61C-1114-

HOH

71C-1181-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51429.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Tyrosine phenol-lyase holoenzyme (internal aldimine)
Source: (gene. exp.) Enterobacter agglomerans (bacteria) / Gene: tpl / Plasmid: pTZ19R / Details (production host): pTZ19R carrying tpl / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / Variant (production host): tnaA / References: UniProt: P31011, tyrosine phenol-lyase

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Non-polymers , 5 types, 2107 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 59 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2042 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Description: cubic THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21 % PEG4000, 0.2 M Ammonium Acetate, 0.1 M Sodium Dihydrogen Citrate, 0.12 M Sodium Hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.84 Å / Num. obs: 442369 / % possible obs: 99.6 % / Redundancy: 4.17 % / Biso Wilson estimate: 12.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.073 / Net I/σ(I): 12.01
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 70556 / CC1/2: 0.856 / Rrim(I) all: 0.515 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C7G

1c7g


Resolution: 1.3→45.84 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.8688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1547 22117 5 %
Rwork0.1278 420226 -
obs0.1292 442343 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.34 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14420 0 316 2042 16778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004715565
X-RAY DIFFRACTIONf_angle_d0.841520970
X-RAY DIFFRACTIONf_chiral_restr0.07532238
X-RAY DIFFRACTIONf_plane_restr0.00492728
X-RAY DIFFRACTIONf_dihedral_angle_d19.51145984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.28667000.247113291X-RAY DIFFRACTION95.37
1.31-1.330.24987340.206113950X-RAY DIFFRACTION99.76
1.33-1.340.22627320.187313912X-RAY DIFFRACTION99.81
1.34-1.360.21437330.174613916X-RAY DIFFRACTION99.82
1.36-1.380.20537330.165913947X-RAY DIFFRACTION99.74
1.38-1.40.19397320.15613917X-RAY DIFFRACTION99.76
1.4-1.420.1857340.147113934X-RAY DIFFRACTION99.82
1.42-1.440.18927330.141413933X-RAY DIFFRACTION99.81
1.44-1.460.17017340.133413937X-RAY DIFFRACTION99.89
1.46-1.480.16477360.126513979X-RAY DIFFRACTION99.86
1.48-1.510.1637350.126413984X-RAY DIFFRACTION99.87
1.51-1.540.15777320.124313915X-RAY DIFFRACTION99.92
1.54-1.570.16017400.121914061X-RAY DIFFRACTION99.97
1.57-1.60.167350.114813956X-RAY DIFFRACTION99.96
1.6-1.630.14917360.109313992X-RAY DIFFRACTION99.96
1.63-1.670.14367390.107114037X-RAY DIFFRACTION99.95
1.67-1.710.14777370.109413996X-RAY DIFFRACTION99.97
1.71-1.760.14577380.111614020X-RAY DIFFRACTION99.97
1.76-1.810.15197370.113214011X-RAY DIFFRACTION99.96
1.81-1.870.15247390.115514032X-RAY DIFFRACTION99.9
1.87-1.930.14077380.114514040X-RAY DIFFRACTION99.88
1.93-2.010.14727390.117414026X-RAY DIFFRACTION99.8
2.01-2.10.14947410.118214076X-RAY DIFFRACTION99.82
2.1-2.210.14237240.116713767X-RAY DIFFRACTION97.93
2.21-2.350.14717410.120714076X-RAY DIFFRACTION99.62
2.35-2.540.14697440.128314144X-RAY DIFFRACTION99.94
2.54-2.790.15047480.130614200X-RAY DIFFRACTION99.92
2.79-3.190.1547460.13214175X-RAY DIFFRACTION99.82
3.19-4.020.14137540.123514321X-RAY DIFFRACTION99.85
4.02-45.840.15027730.135714681X-RAY DIFFRACTION99.5

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