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Open data
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Basic information
Entry | Database: PDB / ID: 1tpl | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF TYROSINE PHENOL-LYASE | ||||||
![]() | TYROSINE PHENOL-LYASE | ||||||
![]() | LYASE(CARBON-CARBON) | ||||||
Function / homology | ![]() tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Antson, A. / Demidkina, T. / Dauter, Z. / Harutyunyan, E. / Wilson, K. | ||||||
![]() | ![]() Title: Three-dimensional structure of tyrosine phenol-lyase. Authors: Antson, A.A. / Demidkina, T.V. / Gollnick, P. / Dauter, Z. / von Tersch, R.L. / Long, J. / Berezhnoy, S.N. / Phillips, R.S. / Harutyunyan, E.H. / Wilson, K.S. #1: ![]() 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 |
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Remark 700 | SHEET 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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 148.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 398.4 KB | Display | ![]() |
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Full document | ![]() | 432.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: 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 |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (-0.5621, -0.8271),Details | THE 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 | Mass: 51508.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: P31012, UniProt: P31013*PLUS, tyrosine phenol-lyase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 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.
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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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
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