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- PDB-1c7g: TYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA -

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Basic information

Entry
Database: PDB / ID: 1c7g
TitleTYROSINE PHENOL-LYASE FROM ERWINIA HERBICOLA
ComponentsTYROSINE PHENOL-LYASE
KeywordsLYASE / TYROSINE DEGRADATION / PYRIDOXAL 5'-PHOSPHATE DEPENDENT
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 / 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
PYRIDOXAL-5'-PHOSPHATE / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesPantoea agglomerans pv. gypsophilae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMikami, B. / Yamamoto, Y. / Katayama, T. / Suzuki, H.
CitationJournal: To be Published
Title: The Structure of Tyrosine Phenol-Lyase from Erwinia Herbicola
Authors: Mikami, B. / Yamamoto, Y. / Katayama, T. / Suzuki, H. / Kumagai, H.
History
DepositionFeb 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 9, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
C: TYROSINE PHENOL-LYASE
D: TYROSINE PHENOL-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,7078
Polymers205,7194
Non-polymers9894
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19490 Å2
ΔGint-82 kcal/mol
Surface area58260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.490, 113.040, 101.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
TYROSINE PHENOL-LYASE /


Mass: 51429.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL 5'-PHOSPHATE LINK TO A 257, B 257, C 257 AND D 257
Source: (gene. exp.) Pantoea agglomerans pv. gypsophilae (bacteria)
Species: Pantoea agglomerans / Strain: pv. gypsophilae / Description: RECOMBINANT GENE / Variant: AJ2985 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / Variant (production host): TNA DEFICIENT / References: UniProt: P31011, tyrosine phenol-lyase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.3 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.2
Details: 30% PEG6000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 6.2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1998
RadiationMonochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.007→42 Å / Num. obs: 113432 / % possible obs: 90.31 % / Observed criterion σ(I): 1 / Redundancy: 4.59 % / Rsym value: 0.102 / Net I/σ(I): 1.34
Reflection shellResolution: 2.007→2.079 Å / % possible all: 53.7

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
X-PLORmodel building
X-PLOR3.85refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TPL

1tpl


Resolution: 2.1→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -8.006 %RANDOM
Rwork0.1862 ---
obs0.1862 84494 78.57 %-
Displacement parametersBiso mean: 19.16 Å2
Refine analyzeLuzzati coordinate error obs: 22 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14420 0 60 425 14905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.442
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.875
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 773 10.12 %
Rwork0.236 6865 -
obs--57.49 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO

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