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- PDB-6mme: Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydro... -

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Basic information

Entry
Database: PDB / ID: 6mme
TitleCitrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from S-ethyl-L-cysteine
ComponentsTyrosine phenol-lyase
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-0JO / pyridin-4-ol / : / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPhillips, R.S.
CitationJournal: Acs Catalysis / Year: 2020
Title: Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics
Authors: Phillips, R.S. / Crasi, S. / Kovalevsky, A. / Gerlits, O. / Weiss, K. / Iorgu, A.I. / Heyes, D.J. / Hay, S.
History
DepositionSep 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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.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
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)104,45610
Polymers103,1342
Non-polymers1,3228
Water10,665592
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)208,91220
Polymers206,2674
Non-polymers2,64516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area20590 Å2
ΔGint-66 kcal/mol
Surface area55220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.720, 133.300, 144.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 51566.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Plasmid: pLATE11-TPL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CQG / pyridin-4-ol


Mass: 95.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5NO
#4: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N2O7P
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine-hCl, pH 8.0, 0.2 M KCl, 0.5 mM PLP, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→55.175 Å / Num. obs: 90235 / % possible obs: 98.61 % / Redundancy: 21.8 % / CC1/2: 1 / Rmerge(I) obs: 0.1178 / Rpim(I) all: 0.02578 / Rrim(I) all: 0.1206 / Net I/σ(I): 18.16
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 22.4 % / Rmerge(I) obs: 4.442 / Num. unique obs: 8809 / CC1/2: 0.401 / Rpim(I) all: 0.951 / Rrim(I) all: 4.544 / % possible all: 97.61

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLF

2vlf


Resolution: 1.9→55.175 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.1982 2008 2.23 %
Rwork0.1635 --
obs0.1643 90200 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.28 Å2 / Biso mean: 52.5756 Å2 / Biso min: 19.2 Å2
Refinement stepCycle: final / Resolution: 1.9→55.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 87 592 7887
Biso mean--64.06 59.67 -
Num. residues----910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.94760.35091530.34016119627298
1.9476-2.00020.31921370.30466189632698
2.0002-2.05910.28741370.27636213635098
2.0591-2.12560.27221400.24036164630498
2.1256-2.20150.29681390.21946212635198
2.2015-2.28970.28671420.20796223636598
2.2897-2.39390.2541430.19026276641999
2.3939-2.52010.24231500.17986237638799
2.5201-2.6780.22741310.15956282641399
2.678-2.88470.20051420.15576351649399
2.8847-3.1750.19281490.15496346649599
3.175-3.63440.19211490.14356378652799
3.6344-4.57860.14841430.126764916634100
4.5786-55.19810.1711530.15756711686499
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)
12.8394-1.45250.56423.7148-0.38221.91780.03780.2504-0.0107-0.19550.07910.7654-0.1854-0.8351-0.11460.31980.0619-0.01070.60080.0840.389638.85113.9573-17.4369
23.40312.4308-0.99764.0136-1.13657.2870.1546-0.21060.08480.3191-0.2242-0.3134-0.34340.45660.05740.19570.0294-0.00560.25320.01890.317864.384311.11432.3156
30.86370.3025-0.1221.5896-0.49322.02320.08920.07820.32680.0862-0.0795-0.1774-0.6340.3143-0.00740.4249-0.06510.03610.35960.05690.423164.10128.3635-11.9056
42.9877-1.172-0.57322.8749-0.3452.85240.17180.38930.7599-0.09990.05280.488-0.9608-0.8081-0.16990.6530.17230.02880.62670.17430.635840.282227.9864-23.8433
52.16391.4280.77622.91170.83632.46920.0949-0.1538-0.17650.2390.1402-0.4709-0.02270.4955-0.20910.2627-0.0044-0.0110.3962-0.05380.272362.30126.525120.0709
60.94280.0991-0.19721.45340.49692.02040.117-0.18240.3560.0521-0.12370.2837-0.6126-0.43910.01570.42760.11650.04910.4392-0.08280.464739.03724.176715.1454
72.85731.36140.46472.80751.07432.78860.0433-0.29730.41140.22830.0231-0.1774-0.3960.3558-0.08510.4155-0.0286-00.3936-0.08390.325960.965217.408530.0366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )A2 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 88 )A58 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 331 )A89 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 456 )A332 - 456
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 57 )B2 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 311 )B58 - 311
7X-RAY DIFFRACTION7chain 'B' and (resid 312 through 456 )B312 - 456

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