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- PDB-6nv8: Perdeuterated tyrosine phenol-lyase from Citrobacter freundii com... -

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Basic information

Entry
Database: PDB / ID: 6nv8
TitlePerdeuterated tyrosine phenol-lyase from Citrobacter freundii complexed with an aminoacrylate intermediate formed from S-ethyl-L-cysteine and 4-hydroxypyridine
Components(Tyrosine phenol- ...) x 2
Keywordslyase/lyase inhibitor / pyridoxal-5'-phosphate / aminoacrylate intermediate / 4-hydroxypyridine / LYASE / lyase-lyase inhibitor complex
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 / 2-AMINO-ACRYLIC ACID / : / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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. / Craig, S. / Kovalevsky, A. / Gerlits, O. / Weiss, K. / Iorgu, A.I. / Heyes, D.J. / Hay, S.
History
DepositionFeb 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
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)104,45510
Polymers103,3622
Non-polymers1,0938
Water4,684260
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)208,91020
Polymers206,7234
Non-polymers2,18616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area20420 Å2
ΔGint-75 kcal/mol
Surface area55380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.350, 143.110, 133.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 13 or resid 42...
21(chain B and (resid 2 through 13 or resid 42...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 13 or resid 42...A2 - 13
121(chain A and (resid 2 through 13 or resid 42...A42 - 65
131(chain A and (resid 2 through 13 or resid 42...A67 - 78
141(chain A and (resid 2 through 13 or resid 42...A80 - 81
151(chain A and (resid 2 through 13 or resid 42...A83 - 256
161(chain A and (resid 2 through 13 or resid 42...A258 - 275
171(chain A and (resid 2 through 13 or resid 42...A277 - 287
181(chain A and (resid 2 through 13 or resid 42...A289 - 309
191(chain A and (resid 2 through 13 or resid 42...A311 - 348
1101(chain A and (resid 2 through 13 or resid 42...A350
1111(chain A and (resid 2 through 13 or resid 42...A1458 - 16
211(chain B and (resid 2 through 13 or resid 42...B2 - 13
221(chain B and (resid 2 through 13 or resid 42...B42 - 65
231(chain B and (resid 2 through 13 or resid 42...B67 - 78
241(chain B and (resid 2 through 13 or resid 42...B80 - 81
251(chain B and (resid 2 through 13 or resid 42...B289 - 309
261(chain B and (resid 2 through 13 or resid 42...B311 - 348
271(chain B and (resid 2 through 13 or resid 42...B350
281(chain B and (resid 2 through 13 or resid 42...B369 - 421
291(chain B and (resid 2 through 13 or resid 42...B423 - 427
2101(chain B and (resid 2 through 13 or resid 42...B1457 - 1501

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Components

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

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


Mass: 51566.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P31013, tyrosine phenol-lyase
#2: Protein Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51794.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: 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 , 6 types, 268 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 95.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5NO
#5: 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.: 1 / Source method: obtained synthetically / Formula: C11H13N2O7P
#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: Chemical ChemComp-DHA / 2-AMINO-ACRYLIC ACID / 2,3-DIDEHYDROALANINE


Type: peptide linking / Mass: 87.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine hydrochloride, pH 8.0, 0.2 M KCl, 1 mM DTT, 0.5 mM pyridoxal-5'-phosphate, 40% PEG 5000 MME

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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: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→42.45 Å / Num. obs: 54045 / % possible obs: 99.85 % / Redundancy: 6.5 % / Biso Wilson estimate: 62.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08448 / Rpim(I) all: 0.03601 / Rrim(I) all: 0.09199 / Net I/σ(I): 12.88
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 6.1 % / Rmerge(I) obs: 2.155 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 5325 / CC1/2: 0.33 / Rpim(I) all: 0.9429 / Rrim(I) all: 2.356 / % possible all: 99.83

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Processing

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

2vlf


Resolution: 2.26→42.45 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2157 2003 3.71 %
Rwork0.1716 --
obs0.1732 54005 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 223.01 Å2 / Biso mean: 80.9239 Å2 / Biso min: 19.36 Å2
Refinement stepCycle: final / Resolution: 2.26→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 0 72 260 7555
Biso mean--98.63 78.38 -
Num. residues----910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3474X-RAY DIFFRACTION7.396TORSIONAL
12B3474X-RAY DIFFRACTION7.396TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.26-2.31650.3851490.337236393788
2.3165-2.37910.36821360.32336903826
2.3791-2.44910.36041390.301836513790
2.4491-2.52820.3761440.280336473791
2.5282-2.61850.30161460.239136783824
2.6185-2.72330.2631400.220936893829
2.7233-2.84730.23981400.201236743814
2.8473-2.99730.26921370.194636953832
2.9973-3.18510.24871510.168837073858
3.1851-3.43090.21921360.168337033839
3.4309-3.7760.19241410.150137463887
3.776-4.32190.1931420.132737483890
4.3219-5.44330.16961530.138437803933
5.4433-42.4570.19571490.174539554104
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)
13.5761.49772.35543.51371.29154.5666-0.09640.126-0.1607-0.364-0.11781.17920.0617-0.88490.20460.5429-0.0119-0.10070.6389-0.11460.92528.9287-17.351552.8234
20.982-0.4941-0.35093.4670.92881.69080.15510.4086-0.1356-0.7946-0.0393-0.3291-0.11130.0751-0.11090.61720.06870.03580.5993-0.07590.531934.1528-9.80640.2645
34.0294-0.3881.1894.32671.35951.37120.25561.3251-0.4617-1.7388-0.68931.532-0.3447-0.51410.06131.1410.1385-0.35810.9795-0.33790.994613.6798-24.35837.3631
42.9769-2.53081.75494.4936-2.20854.38180.13590.1743-0.7105-0.9291-0.07161.37550.393-1.2284-0.08420.8827-0.0463-0.27170.8931-0.26440.95095.883-22.168839.1014
55.14171.9589-2.34762.7807-1.40363.51380.0549-0.18120.1465-0.2541-0.195-0.6771-0.22480.37170.15970.54460.02630.06530.44940.05390.750132.3520.029260.4318
63.782-0.00121.234.5080.8783.34750.18970.2918-0.0019-0.33610.11350.60210.2651-0.3093-0.27470.4964-0.0285-0.04720.60440.04380.67579.28690.75355.3663
71.0656-0.45250.00172.5994-0.38321.63790.15070.42720.2344-0.68470.07760.601-0.0792-0.3089-0.22550.66320.0628-0.09890.68650.17020.717810.02418.674442.3646
82.80150.7494-1.0584.4194-1.482.66120.05720.48120.4347-0.6233-0.0122-0.6052-0.13150.1913-0.05230.7081-0.00360.12260.59010.11650.722233.696530.15747.8042
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 331 )A58 - 331
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 413 )A332 - 413
4X-RAY DIFFRACTION4chain 'A' and (resid 414 through 456 )A414 - 456
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 57 )B2 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 88 )B58 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 331 )B89 - 331
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 456 )B332 - 456

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