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

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Basic information

Entry
Database: PDB / ID: 6mqq
TitleCitrobacter freundii F448A mutant 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: 2.05 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
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_ncs_dom_lim
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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,92510
Polymers102,6032
Non-polymers1,3228
Water6,197344
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)207,85020
Polymers205,2064
Non-polymers2,64516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area20300 Å2
ΔGint-76 kcal/mol
Surface area55610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.560, 133.850, 144.520
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 65 or resid 67...
21(chain B and (resid 2 through 65 or resid 67...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNMETMET(chain A and (resid 2 through 65 or resid 67...AA2 - 651 - 64
12GLYGLYTYRTYR(chain A and (resid 2 through 65 or resid 67...AA67 - 7866 - 77
13LEULEUTHRTHR(chain A and (resid 2 through 65 or resid 67...AA80 - 25279 - 251
14SERSERPHEPHE(chain A and (resid 2 through 65 or resid 67...AA254 - 275253 - 274
15ALAALAGLYGLY(chain A and (resid 2 through 65 or resid 67...AA386 - 423385 - 422
16ILEILEGLNGLN(chain A and (resid 2 through 65 or resid 67...AA425 - 429424 - 428
17LYSLYSILEILE(chain A and (resid 2 through 65 or resid 67...AA431 - 456430 - 455
21ASNASNMETMET(chain B and (resid 2 through 65 or resid 67...BB2 - 651 - 64
22GLYGLYTYRTYR(chain B and (resid 2 through 65 or resid 67...BB67 - 7866 - 77
23LEULEUTHRTHR(chain B and (resid 2 through 65 or resid 67...BB80 - 25279 - 251
24SERSERPHEPHE(chain B and (resid 2 through 65 or resid 67...BB254 - 275253 - 274
25SERSERTYRTYR(chain B and (resid 2 through 65 or resid 67...BB277 - 285276 - 284
26GLYGLYILEILE(chain B and (resid 2 through 65 or resid 67...BB287 - 384286 - 383
27ALAALAGLYGLY(chain B and (resid 2 through 65 or resid 67...BB386 - 423385 - 422
28ILEILEGLNGLN(chain B and (resid 2 through 65 or resid 67...BB425 - 429424 - 428
29LYSLYSILEILE(chain B and (resid 2 through 65 or resid 67...BB431 - 456430 - 455

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 51301.461 Da / Num. of mol.: 2 / 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-CQG / pyridin-4-ol


Mass: 95.099 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5NO
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#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.: 344 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
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: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→45.96 Å / Num. obs: 73245 / % possible obs: 99.83 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1031 / Rpim(I) all: 0.02926 / Rrim(I) all: 0.1073 / Net I/σ(I): 14.49
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 13.9 % / Rmerge(I) obs: 3.758 / Num. unique obs: 7242 / CC1/2: 0.243 / Rpim(I) all: 1.034 / Rrim(I) all: 3.9 / % possible all: 99.72

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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: 2.05→45.96 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.1967 2000 2.73 %
Rwork0.1758 --
obs0.1763 73231 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.97 Å2 / Biso mean: 72.941 Å2 / Biso min: 31.86 Å2
Refinement stepCycle: final / Resolution: 2.05→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 87 344 7627
Biso mean--83.74 70.83 -
Num. residues----910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4152X-RAY DIFFRACTION6.943TORSIONAL
12B4152X-RAY DIFFRACTION6.943TORSIONAL
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 (%)
2.0499-2.10120.39941450.362449885133100
2.1012-2.1580.32481460.33250175163100
2.158-2.22150.34451370.302250505187100
2.2215-2.29320.29161420.271850385180100
2.2932-2.37520.28911380.251150325170100
2.3752-2.47030.27381380.237950375175100
2.4703-2.58270.25751440.217150485192100
2.5827-2.71880.2271430.1950625205100
2.7188-2.88910.2381440.178750565200100
2.8891-3.11220.21551400.172551105250100
3.1122-3.42530.20251400.169750885228100
3.4253-3.92070.15211490.15765119526899
3.9207-4.93870.14341440.137852015345100
4.9387-45.97150.18841500.162453855535100
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)
12.5583-0.5657-0.4112.8373-2.24892.9508-0.06770.430.0834-0.01610.51190.7664-0.1893-1.4044-0.18880.42750.0593-0.05130.87920.130.5611-17.543-54.555-17.54
22.77672.02180.42753.7291-0.52056.52360.0008-0.1283-0.01530.2513-0.1639-0.2468-0.33380.44210.15980.35130.024-0.00130.460.0150.51524.836-55.8082.077
30.9494-0.3062-0.14631.95130.44694.61350.11620.02370.36460.0201-0.11360.1279-1.3589-0.05290.02790.9352-0.0548-0.00870.53810.08310.71860.249-32.143-11.758
42.2597-1.0932-0.40343.1246-0.3813.2460.1596-0.04820.41970.1931-0.1617-0.4888-1.02680.4371-0.00260.7471-0.17990.01220.52560.13650.54928.273-32.938-16.78
51.60670.68860.11311.523-0.79424.8456-0.0080.0860.42290.010.03930.0747-0.8622-0.15230.09070.54320.03360.01980.36720.07920.5262-4.08-43.664-16.286
63.0819-1.1413-2.29415.38061.68434.6262-0.01450.23010.70550.07470.62431.1044-1.144-1.4196-0.24710.90780.33520.04050.96180.33330.9358-22.057-41.914-24.144
74.8342.1367-0.01122.72751.25012.83290.0023-0.2641-0.06640.1570.2427-0.419-0.19960.6562-0.23770.39540.0204-0.01670.564-0.05340.39662.368-59.5519.927
80.93760.1928-1.00331.0019-0.3743.2350.1573-0.17510.46790.1654-0.03210.05-1.14390.0243-0.08740.79820.09140.02380.5669-0.06830.7241-17.204-42.17612.75
92.07870.68360.28772.5679-0.48512.20450.289-0.12690.7640.0685-0.17070.3012-1.1632-0.2831-0.11241.01370.1980.22010.6746-0.12180.7806-23.791-37.39123.558
101.21230.0387-0.14941.12810.11933.12030.0701-0.07140.29690.0777-0.02380.2629-0.5734-0.4165-0.01540.52920.07350.10490.4912-0.05710.5958-15.542-48.97918.514
113.32360.9527-0.1992.0137-0.023.7665-0.1126-0.12770.5374-0.0240.2328-0.1364-1.22940.7858-0.09280.7275-0.110.01720.5087-0.08140.48732.007-45.29326.624
125.17163.7889-1.91648.1274-0.26074.3557-0.0735-0.50260.1723-0.31680.3403-1.0656-0.60341.3639-0.1520.6172-0.13720.06260.7891-0.2110.58748.239-49.36429.703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:57 )A2 - 57
2X-RAY DIFFRACTION2( CHAIN A AND RESID 58:88 )A58 - 88
3X-RAY DIFFRACTION3( CHAIN A AND RESID 89:159 )A89 - 159
4X-RAY DIFFRACTION4( CHAIN A AND RESID 160:228 )A160 - 228
5X-RAY DIFFRACTION5( CHAIN A AND RESID 229:413 )A229 - 413
6X-RAY DIFFRACTION6( CHAIN A AND RESID 414:456 )A414 - 456
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:57 )B2 - 57
8X-RAY DIFFRACTION8( CHAIN B AND RESID 58:159 )B58 - 159
9X-RAY DIFFRACTION9( CHAIN B AND RESID 160:228 )B160 - 228
10X-RAY DIFFRACTION10( CHAIN B AND RESID 229:361 )B229 - 361
11X-RAY DIFFRACTION11( CHAIN B AND RESID 362:413 )B362 - 413
12X-RAY DIFFRACTION12( CHAIN B AND RESID 414:456 )B414 - 456

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