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

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Basic information

Entry
Database: PDB / ID: 6dyt
TitleCitrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine
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-F0G / : / ALANYL-PYRIDOXAL-5'-PHOSPHATE / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionJul 2, 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_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)103,9087
Polymers102,8652
Non-polymers1,0435
Water11,223623
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)207,81714
Polymers205,7314
Non-polymers2,08610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area20220 Å2
ΔGint-75 kcal/mol
Surface area56920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.640, 133.270, 145.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
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 - 652 - 65
12GLYGLYALAALA(chain A and (resid 2 through 65 or resid 67...AA67 - 21567 - 215
13ARGARGGLUGLU(chain A and (resid 2 through 65 or resid 67...AA217 - 273217 - 273
14PHEPHETYRTYR(chain A and (resid 2 through 65 or resid 67...AA275 - 285275 - 285
15ASNASNILEILE(chain A and (resid 2 through 65 or resid 67...AA2 - 4562 - 456
16PROPROILEILE(chain A and (resid 2 through 65 or resid 67...AA289 - 384289 - 384
17ALAALAGLNGLN(chain A and (resid 2 through 65 or resid 67...AA386 - 429386 - 429
18LYSLYSILEILE(chain A and (resid 2 through 65 or resid 67...AA431 - 456431 - 456
21ASNASNMETMET(chain B and (resid 2 through 65 or resid 67...BB2 - 652 - 65
22GLYGLYALAALA(chain B and (resid 2 through 65 or resid 67...BB67 - 21567 - 215
23ARGARGGLUGLU(chain B and (resid 2 through 65 or resid 67...BB217 - 273217 - 273
24PHEPHETYRTYR(chain B and (resid 2 through 65 or resid 67...BB275 - 285275 - 285
25GLYGLYGLYGLY(chain B and (resid 2 through 65 or resid 67...BB287287
26PROPROILEILE(chain B and (resid 2 through 65 or resid 67...BB289 - 384289 - 384
27ALAALAGLNGLN(chain B and (resid 2 through 65 or resid 67...BB386 - 429386 - 429
28LYSLYSILEILE(chain B and (resid 2 through 65 or resid 67...BB431 - 456431 - 456

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 51432.660 Da / Num. of mol.: 2 / Mutation: F448A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: 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, 628 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: K
#3: Chemical ChemComp-F0G / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine / PLP-Ala


Type: L-peptide linking / Mass: 318.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7P
#4: Chemical ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N2O7P
#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.: 623 / 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: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine-HCl, pH 8, 1 mM EDTA, 5 mM 2-mercaptoethanol, 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: MARRESEARCH / Detector: CCD / Date: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→37.893 Å / Num. obs: 73005 / % possible obs: 98.8 % / Redundancy: 5.016 % / Biso Wilson estimate: 56.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.107 / Χ2: 1.08 / Net I/σ(I): 7.52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.1235.233.5510.4246210.1863.86199.6
2.123-2.275.21.9551.0245110.3422.1899.6
2.27-2.335.1361.6141.2843870.4141.80299.7
2.33-2.45.0381.2951.6742890.5741.44799.2
2.4-2.484.8871.1671.941380.6581.30998.9
2.48-2.574.3440.8192.4639820.7550.93299.2
2.57-2.675.0920.6893.238790.8360.76999.6
2.67-2.785.4430.5444.2237350.9060.60399.5
2.78-2.95.4140.3955.3935910.9440.43799.3
2.9-3.045.3860.2877.0134330.9580.31999
3.04-3.215.3030.2018.9232510.9750.22498.9
3.21-3.45.1720.14611.330750.9870.16398.4
3.4-3.635.0330.10613.6728890.9880.11898.2
3.63-3.934.5620.08715.8426820.9920.09897.2
3.93-4.34.6540.06918.6625090.9930.07898
4.3-4.814.0760.06618.9722020.990.07495.8
4.81-5.554.560.05820.6220220.9950.06698.3
5.55-6.85.120.0522.1617560.9960.05699.1
6.8-9.6250.04122.9713750.9970.04698.7
9.62-37.8934.5930.03722.067860.9980.04293.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLF

2vlf


Resolution: 2.05→37.893 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.02
RfactorNum. reflection% reflection
Rfree0.2321 1997 2.74 %
Rwork0.1865 --
obs0.1877 72872 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217 Å2 / Biso mean: 80.095 Å2 / Biso min: 36.15 Å2
Refinement stepCycle: final / Resolution: 2.05→37.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 66 623 7885
Biso mean--80.93 82.41 -
Num. residues----910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4138X-RAY DIFFRACTION6.964TORSIONAL
12B4138X-RAY DIFFRACTION6.964TORSIONAL
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 (%)
2.05-2.10120.37321440.37734943508799
2.1012-2.1580.42551440.358750185162100
2.158-2.22150.37661350.35550215156100
2.2215-2.29320.38331350.341650845219100
2.2932-2.37520.34991470.312250305177100
2.3752-2.47030.34521420.292150195161100
2.4703-2.58270.27581470.25215009515699
2.5827-2.71880.25981320.230750745206100
2.7188-2.88910.20081420.203950565198100
2.8891-3.11210.24791550.191250845239100
3.1121-3.42510.2551360.187150895225100
3.4251-3.92020.21821460.16425124527099
3.9202-4.93740.19981400.13794937507795
4.9374-37.89990.1961520.161153875539100
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)
14.5651-1.3992-0.04785.4196-2.74822.83510.00730.53850.2657-0.13470.55960.79470.0297-1.3341-0.39480.51420.0113-0.07140.9440.11990.5039-17.7618-53.7431-17.4761
25.19084.71521.33476.7406-1.27978.05680.3277-0.583-0.34660.3361-0.5475-0.6953-0.43190.69680.17610.39430.0596-0.0020.46210.0020.48794.7213-55.19322.1478
31.32750.06460.54144.3872-3.41265.7970.09360.17490.53290.31930.01730.4344-1.17310.0434-0.12450.8789-0.0575-0.00510.55580.0560.7254-0.4471-30.8619-7.9955
43.18130.53970.26363.88822.58914.12560.01460.2290.4976-0.1674-0.0499-0.3274-0.65330.37890.05070.676-0.1373-0.04620.55840.19520.57187.3437-32.5705-18.3773
54.96370.0618-2.32593.71860.43234.75930.214-0.04780.40210.1063-0.0767-0.4281-0.92470.7795-0.12420.6109-0.0594-0.0630.60340.12870.52728.0152-41.9208-6.6374
62.18260.3024-1.65632.017-0.98695.47530.16750.51260.6419-0.19590.15010.4114-0.9635-0.7908-0.03370.62850.0848-0.01290.48520.13470.608-9.5696-43.4715-20.0732
74.6542-2.8684-4.22857.943.0756.45490.08710.82770.82840.23090.55491.2919-0.8972-2.0558-0.30250.86460.33280.07231.19460.36251.0747-22.398-41.0857-23.8097
83.68590.88341.49542.48411.19723.4218-0.0102-0.16640.08690.21520.2535-0.4531-0.16180.767-0.25810.47260.01160.03380.6265-0.06570.392.3116-59.609420.034
92.2735-0.4407-0.96643.48022.39813.6920.1364-0.18290.61170.2099-0.03670.0628-0.675-0.1307-0.05570.72240.07040.02190.5837-0.01150.6947-17.1519-41.601110.3505
102.5897-0.16170.10763.2514-3.68114.6418-0.1505-0.72870.87480.6743-0.0008-0.0113-1.1321-0.39610.12680.98780.12520.17870.8297-0.33210.888-23.2675-34.710127.0256
114.1082-1.7624-0.13418.0865-0.57834.19690.2505-0.28650.41680.51390.00790.7472-0.4694-1.0096-0.28870.54690.070.12260.8582-0.1720.6815-26.5487-47.950622.5767
121.2037-0.0819-0.21111.238-0.51064.1841-0.0104-0.00870.3896-0.0964-0.12230.2105-0.4362-0.56220.08210.46530.03880.03630.5339-0.0530.5368-17.1956-49.218111.546
136.44364.48331.95274.78760.13342.70090.3259-0.80060.78480.454-0.29720.1221-0.54950.1104-0.03580.786-0.06230.07250.8595-0.19540.5926-0.3268-46.699236.4459
143.62240.9055-0.20522.68170.53153.2748-0.112-0.45850.6516-0.12470.10080.0893-1.14280.77510.02420.6999-0.16950.01540.5301-0.12290.44452.0443-45.354426.8794
157.77716.5922-2.45289.1251-1.53757.51370.0838-0.6520.0295-0.06530.001-0.8716-0.68231.1847-0.14780.60070.00860.02840.7033-0.17920.58988.3571-49.600929.9547
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 146 )A89 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 228 )A147 - 228
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 285 )A229 - 285
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 413 )A286 - 413
7X-RAY DIFFRACTION7chain 'A' and (resid 414 through 456 )A414 - 456
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 57 )B2 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 146 )B58 - 146
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 207 )B147 - 207
11X-RAY DIFFRACTION11chain 'B' and (resid 208 through 247 )B208 - 247
12X-RAY DIFFRACTION12chain 'B' and (resid 248 through 331 )B248 - 331
13X-RAY DIFFRACTION13chain 'B' and (resid 332 through 361 )B332 - 361
14X-RAY DIFFRACTION14chain 'B' and (resid 362 through 413 )B362 - 413
15X-RAY DIFFRACTION15chain 'B' and (resid 414 through 456 )B414 - 456

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