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- PDB-6ecg: Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed... -

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Basic information

Entry
Database: PDB / ID: 6ecg
TitleCitrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-methionine
Components(Tyrosine phenol- ...) x 2
KeywordsLYASE / pyridoxal-5'-phosphate / aminotransferase fold
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 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, 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 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Chem-PM9 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPhillips, R.S.
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism.
Authors: Phillips, R.S. / Craig, S.
History
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)103,7647
Polymers102,8312
Non-polymers9335
Water11,692649
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)207,52814
Polymers205,6624
Non-polymers1,86610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area20940 Å2
ΔGint-66 kcal/mol
Surface area55540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.610, 132.850, 144.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Tyrosine phenol- ... , 2 types, 2 molecules AB

#1: Protein Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51301.461 Da / Num. of mol.: 1 / Mutation: F448A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Plasmid: pLATE11-tpl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase
#2: Protein Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51529.578 Da / Num. of mol.: 1 / Mutation: F448A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Plasmid: pLATE11-tpl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 5 types, 654 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PM9 / (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}-4-(METHYLSULFANYL)BUTANOIC ACID


Mass: 378.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine-HCl, pH 8.0, 0.2 M KCl, 1 mM DTT, 0.5 mM pyridoxal-5'-phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→45.95 Å / Num. obs: 53790 / % possible obs: 99.92 % / Redundancy: 6 % / Biso Wilson estimate: 42.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1189 / Rpim(I) all: 0.05322 / Rrim(I) all: 0.1307 / Net I/σ(I): 7.75
Reflection shellResolution: 2.27→2.351 Å / Redundancy: 6.2 % / Num. unique obs: 5280 / CC1/2: 0.239 / Rpim(I) all: 1.495 / Rrim(I) all: 3.751 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
PDB_EXTRACT3.24data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLH

2vlh


Resolution: 2.27→45.95 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 2005 3.73 %
Rwork0.183 --
obs0.185 53790 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.24 Å2
Refinement stepCycle: LAST / Resolution: 2.27→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7191 0 58 649 7898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.32680.34281350.29853634X-RAY DIFFRACTION100
2.3268-2.38970.30171480.28953671X-RAY DIFFRACTION100
2.3897-2.460.32761440.28353617X-RAY DIFFRACTION100
2.46-2.53940.32321290.26843641X-RAY DIFFRACTION100
2.5394-2.63020.31121500.24543673X-RAY DIFFRACTION100
2.6302-2.73550.26391390.24013674X-RAY DIFFRACTION100
2.7355-2.860.24921430.21753650X-RAY DIFFRACTION100
2.86-3.01070.26561450.20133680X-RAY DIFFRACTION100
3.0107-3.19930.25761400.1883679X-RAY DIFFRACTION100
3.1993-3.44630.22081420.17033682X-RAY DIFFRACTION100
3.4463-3.79290.20521400.14443729X-RAY DIFFRACTION100
3.7929-4.34140.16611570.13093731X-RAY DIFFRACTION100
4.3414-5.46830.15051370.1443776X-RAY DIFFRACTION100
5.4683-45.96010.20591560.18263948X-RAY DIFFRACTION100
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)
13.1224-2.339-0.73342.73751.42092.42460.07330.22690.14380.09490.2578-0.45150.08441.0181-0.33640.40950.03560.00010.7582-0.10110.3879-38.8482-13.265-17.5936
21.0890.33580.06851.32130.54042.22190.0670.1299-0.31950.0134-0.0037-0.01460.6048-0.14970.02540.4598-0.0041-0.03540.3691-0.060.4105-60.9754-26.5327-13.2287
33.7987-0.89331.15310.97291.66475.26580.5850.4181-1.1842-0.21780.0617-0.57541.81471.81020.98480.87130.3627-0.11361.0928-0.34360.8245-39.017-26.7374-22.1621
41.9373-0.29530.51451.6647-0.46670.23070.14070.5795-0.55210.00110.0731-0.63810.87870.80070.05760.83920.3349-0.10260.6778-0.23910.6661-38.3443-25.2278-23.3222
52.13281.3931-1.15053.1105-1.17363.55590.02070.00530.06670.17550.1860.31870.0356-0.5584-0.19450.28780.0074-0.01070.39220.0340.2542-61.9218-7.082819.8632
61.5121-0.05470.39221.7652-0.81512.83650.1523-0.1984-0.42940.0399-0.1086-0.17740.53490.363-0.01160.40630.0963-0.05240.43160.06430.4749-39.1351-24.313714.7858
72.70271.3459-0.3432.5813-1.182.7486-0.0365-0.3733-0.27630.08810.03290.14030.4112-0.3442-0.02420.4501-0.0337-0.00380.43530.07250.3218-60.7041-17.632629.808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 58 THROUGH 361 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 362 THROUGH 397 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 398 THROUGH 456 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 2 THROUGH 57 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 58 THROUGH 311 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 312 THROUGH 456 )

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