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- PDB-2tpl: TYROSINE PHENOL-LYASE FROM CITROBACTER INTERMEDIUS COMPLEX WITH 3... -

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Basic information

Entry
Database: PDB / ID: 2tpl
TitleTYROSINE PHENOL-LYASE FROM CITROBACTER INTERMEDIUS COMPLEX WITH 3-(4'-HYDROXYPHENYL)PROPIONIC ACID, PYRIDOXAL-5'-PHOSPHATE AND CS+ ION
ComponentsTYROSINE PHENOL-LYASE
KeywordsLYASE / PLP-DEPENDENT ENZYME / PYRIDOXAL PHOSPHATE
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
: / HYDROXYPHENYL PROPIONIC ACID / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAntson, A.A. / Demidkina, T.V. / Wilson, K.S.
CitationJournal: Biochemistry / Year: 1997
Title: The crystal structure of Citrobacter freundii tyrosine phenol-lyase complexed with 3-(4'-hydroxyphenyl)propionic acid, together with site-directed mutagenesis and kinetic analysis, ...Title: The crystal structure of Citrobacter freundii tyrosine phenol-lyase complexed with 3-(4'-hydroxyphenyl)propionic acid, together with site-directed mutagenesis and kinetic analysis, demonstrates that arginine 381 is required for substrate specificity.
Authors: Sundararaju, B. / Antson, A.A. / Phillips, R.S. / Demidkina, T.V. / Barbolina, M.V. / Gollnick, P. / Dodson, G.G. / Wilson, K.S.
History
DepositionJan 23, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 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 / struct_ref_seq_dif / struct_site
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.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.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_asym_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_ref_seq_dif.details / _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: TYROSINE PHENOL-LYASE
B: TYROSINE PHENOL-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9065
Polymers103,4742
Non-polymers4323
Water4,540252
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)207,81110
Polymers206,9474
Non-polymers8646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20010 Å2
ΔGint-243 kcal/mol
Surface area56270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.070, 143.910, 59.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.978, -0.208, -0.004), (-0.208, -0.978, 0.001), (-0.004, -1)
Vector: 0.04996, -0.09492, 15.28941)

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Components

#1: Protein TYROSINE PHENOL-LYASE


Mass: 51736.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Citrobacter freundii (bacteria) / References: UniProt: P31013, tyrosine phenol-lyase
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-HPP / HYDROXYPHENYL PROPIONIC ACID


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 8
Details: 30-45% PEG 5000 MONOMETHYL ETHER, 0.4 M CSCL, 50 MM TRIETHANOLAMINE BUFFER PH 8.0, 1 MM DTT, 0.2 MM PLP, 50 MM HPPA
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution is half diluted with a reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
250 mMHPPA1drop
350 mMtriethanolamine1drop
41 mMdithiothreitol1drop
520000 MPLP1drop
630-45 %(w/v)mPEG1reservoir
70.15-0.6 M1reservoiror CsClKCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9177
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: PT-COATED TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 33108 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.9 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TYROSINE PHENOL-LYASE HOLOENZYME

Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 -3 %RANDOM
Rwork0.183 ---
obs-32151 78.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 14 252 7504
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 957
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_mcbond_it2.53
X-RAY DIFFRACTIONp_scbond_it9.68
X-RAY DIFFRACTIONp_mcangle_it3.44
X-RAY DIFFRACTIONp_scangle_it11.210

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