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- PDB-2ez1: Holo tyrosine phenol-lyase from Citrobacter freundii at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 2ez1
TitleHolo tyrosine phenol-lyase from Citrobacter freundii at pH 8.0
ComponentsTyrosine phenol-lyase
KeywordsLYASE / PLP-dependent enzyme / pyridoxal-5'-phosphate / domain closure
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMilic, D. / Matkovic-Calogovic, D. / Demidkina, T.V. / Antson, A.A.
CitationJournal: Biochemistry / Year: 2006
Title: Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions
Authors: Milic, D. / Matkovic-Calogovic, D. / Demidkina, T.V. / Kulikova, V.V. / Sinitzina, N.I. / Antson, A.A.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6684
Polymers103,5902
Non-polymers782
Water16,250902
1
A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules

A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,3368
Polymers207,1804
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area19190 Å2
ΔGint-82 kcal/mol
Surface area57690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.860, 143.850, 60.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: 133.860-x, 143.850-y, z.

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Components

#1: Protein Tyrosine phenol-lyase / E.C.4.1.99.2 / Beta-tyrosinase


Mass: 51794.902 Da / Num. of mol.: 2 / Fragment: Tyrosine phenol-lyase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: TPL / Plasmid: pTZTPL / Production host: Escherichia coli (E. coli) / Strain (production host): SVS370 / References: UniProt: P31013, tyrosine phenol-lyase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.81 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM triethanolamine buffer, 0.5 mM PLP, 2 mM DDT, 0.4 M to 0.8 M KCl, 35 - 38% (w/v) monomethyl ether PEG 5000, pH 8.0, VAPOUR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 22, 1995
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 85710 / Num. obs: 85710 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 / Χ2: 1.061
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 90.7 % / Rmerge(I) obs: 0.359 / Num. measured obs: 4151 / Χ2: 1.049 / % possible all: 90.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.089 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2508 3 %RANDOM
Rwork0.152 ---
all0.153 84762 --
obs0.153 84762 92.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 2 902 8142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227361
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9569929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49523.799358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.324151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5331552
X-RAY DIFFRACTIONr_chiral_restr0.0950.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025624
X-RAY DIFFRACTIONr_nbd_refined0.2060.23381
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2714
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.237
X-RAY DIFFRACTIONr_mcbond_it1.2892.54504
X-RAY DIFFRACTIONr_mcangle_it2.09847223
X-RAY DIFFRACTIONr_scbond_it3.86662903
X-RAY DIFFRACTIONr_scangle_it5.479102705
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 174 -
Rwork0.185 5820 -
all-5994 -
obs--89.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72440.0333-0.47911.13010.44051.2705-0.0406-0.0825-0.10620.314-0.08670.20730.297-0.24740.12730.0231-0.08410.0761-0.0006-0.0055-0.05843.25348.53420.95
20.906-0.26430.37811.2242-0.27261.06440.01220.10990.125-0.06890.01960.1571-0.1647-0.1624-0.0317-0.07720.0515-0.0026-0.04880.0303-0.067149.02199.885-5.439
30.53780.10240.04891.24090.19470.4464-0.0170.06440.0051-0.1384-0.0350.25990.0736-0.16690.052-0.1065-0.0233-0.0146-0.0131-0.0209-0.090639.48262.884-4.83
40.5959-0.0216-0.13051.1390.05870.52420.0299-0.04840.04140.3039-0.02340.2297-0.1382-0.1755-0.0065-0.0190.03910.0796-0.0119-0.0173-0.095842.29986.87420.395
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA19 - 4819 - 48
21AA333 - 456333 - 456
32BB19 - 4819 - 48
42BB333 - 456333 - 456
53AA57 - 31057 - 310
64BB57 - 31057 - 310

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