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- PDB-1tpl: THE THREE-DIMENSIONAL STRUCTURE OF TYROSINE PHENOL-LYASE -

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Basic information

Entry
Database: PDB / ID: 1tpl
TitleTHE THREE-DIMENSIONAL STRUCTURE OF TYROSINE PHENOL-LYASE
ComponentsTYROSINE PHENOL-LYASE
KeywordsLYASE(CARBON-CARBON)
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 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter intermedius (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsAntson, A. / Demidkina, T. / Dauter, Z. / Harutyunyan, E. / Wilson, K.
Citation
#1: Journal: FEBS Lett. / Year: 1992
Title: The Polypeptide Chain Fold in Tyrosine Phenol-Lyase, a Pyridoxal-5'-Phosphate-Dependent Enzyme
Authors: Antson, A.A. / Strokopytov, B.V. / Murshudov, G.N. / Isupov, M.N. / Harutyunyan, E.H. / Demidkina, T.V. / Vassylyev, D.G. / Dauter, Z. / Terry, H. / Wilson, K.S.
History
DepositionNov 25, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET EACH SUBUNIT CONTAINS 14 ALPHA-HELICES AND TWO BETA-SHEETS: LARGE AND SMALL. THE STRUCTURE ...SHEET EACH SUBUNIT CONTAINS 14 ALPHA-HELICES AND TWO BETA-SHEETS: LARGE AND SMALL. THE STRUCTURE ALSO CONTAINS INTERSUBUNIT BETA-SHEET.

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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)103,4026
Polymers103,0182
Non-polymers3844
Water8,107450
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)206,80412
Polymers206,0354
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17400 Å2
ΔGint-190 kcal/mol
Surface area60040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.020, 138.270, 93.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: VAL A 182 - THR A 183 OMEGA =355.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 339
3: VAL B 182 - THR B 183 OMEGA =354.87 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO B 339
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-0.5621, -0.8271), (-0.8271, 0.5621), (-1) / Vector: 59.375, 31.437, 41.345)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS OF THE TETRAMER. COORDINATES FOR OTHER TWO SUBUNITS CAN BE GENERATED USING CRYSTALLOGRAPHIC OPERATOR (76.02-X; -Y; Z). THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*

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Components

#1: Protein TYROSINE PHENOL-LYASE /


Mass: 51508.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter intermedius (bacteria)
References: UniProt: P31012, UniProt: P31013*PLUS, tyrosine phenol-lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
250 mMpotasssium phosphate1drop
320 %satammonium sulfate1drop
40.2 mMdithiothreitol1drop
530 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.058

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→10 Å
Details: ABOUT 6% OF THE AMINO ACIDS HAVE POOR ELECTRON DENSITY AND COULD NOT BE LOCATED. THESE RESIDUES LIE IN THREE LOOPS ON THE SURFACE OF THE MOLECULE: RESIDUES 123 - 131, 384 - 398, 442 - 447 IN ...Details: ABOUT 6% OF THE AMINO ACIDS HAVE POOR ELECTRON DENSITY AND COULD NOT BE LOCATED. THESE RESIDUES LIE IN THREE LOOPS ON THE SURFACE OF THE MOLECULE: RESIDUES 123 - 131, 384 - 398, 442 - 447 IN THE A CHAIN AND RESIDUES 123 - 133, 384 - 398, 442 - 445 IN THE B CHAIN. NO COORDINATES ARE PRESENT FOR THESE RESIDUES.
RfactorNum. reflection
obs0.162 43205
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 20 450 7194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection obs: 43205 / Rfactor obs: 0.1622
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.038
X-RAY DIFFRACTIONp_planar_d0.050.049
X-RAY DIFFRACTIONp_plane_restr0.020.012
X-RAY DIFFRACTIONp_chiral_restr0.20.213
X-RAY DIFFRACTIONp_mcbond_it43.8
X-RAY DIFFRACTIONp_scbond_it88
X-RAY DIFFRACTIONp_mcangle_it65.8
X-RAY DIFFRACTIONp_scangle_it1010.3

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