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- PDB-6dz5: Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed... -

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Basic information

Entry
Database: PDB / ID: 6dz5
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-P61 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 3, 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 1.2Mar 6, 2019Group: Data collection / Database references / Structure summary
Category: entity / struct_ref_seq_dif / Item: _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Oct 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
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

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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)104,1277
Polymers102,8652
Non-polymers1,2615
Water10,124562
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)208,25314
Polymers205,7314
Non-polymers2,52210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area20100 Å2
ΔGint-74 kcal/mol
Surface area56800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 132.810, 145.370
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 65 or resid 67...A2 - 65
121(chain A and (resid 2 through 65 or resid 67...A67 - 78
131(chain A and (resid 2 through 65 or resid 67...A80 - 16
141(chain A and (resid 2 through 65 or resid 67...A291 - 380
151(chain A and (resid 2 through 65 or resid 67...A382 - 429
161(chain A and (resid 2 through 65 or resid 67...A431 - 500
211(chain B and (resid 2 through 65 or resid 67...B2 - 65
221(chain B and (resid 2 through 65 or resid 67...B67 - 78
231(chain B and (resid 2 through 65 or resid 67...B80 - 160
241(chain B and (resid 2 through 65 or resid 67...B162 - 178
251(chain B and (resid 2 through 65 or resid 67...B180 - 289
261(chain B and (resid 2 through 65 or resid 67...B291 - 380
271(chain B and (resid 2 through 65 or resid 67...B382 - 391
281(chain B and (resid 2 through 65 or resid 67...B395 - 429
291(chain B and (resid 2 through 65 or resid 67...B431 - 500

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Components

#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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P61 / (2E)-3-(3-fluoro-4-hydroxyphenyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid


Mass: 428.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18FN2O8P
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine-HCl, pH 8.0, 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: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→44.47 Å / Num. obs: 54544 / % possible obs: 98.7 % / Redundancy: 14.573 % / Biso Wilson estimate: 51.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.224 / Rrim(I) all: 0.232 / Χ2: 0.998 / Net I/σ(I): 10.59 / Num. measured all: 794857 / Scaling rejects: 630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.26-2.3214.9553.4980.8560252402840290.3143.621100
2.32-2.3814.9122.9581.0158904395139500.4553.063100
2.38-2.4514.9252.9011.156505379037860.5013.00499.9
2.45-2.5314.8872.1441.4955231371037100.7152.22100
2.53-2.6114.8551.9071.8253746361936180.7371.975100
2.61-2.714.8671.5822.2951544347034670.8011.63899.9
2.7-2.814.7321.2652.9649719337633750.8731.311100
2.8-2.9214.7140.9673.9347556323232320.921.002100
2.92-3.0514.8780.6865.5146316311631130.9570.7199.9
3.05-3.214.8110.5137.2744434300130000.9750.531100
3.2-3.3714.8440.34810.0442277285028480.9910.3699.9
3.37-3.5714.8540.24513.5240180270627050.9940.254100
3.57-3.8213.9520.1661726677255119120.9970.17375
3.82-4.1314.4860.11923.6734230237023630.9970.12399.7
4.13-4.5214.3020.08130.2231492220922020.9980.08499.7
4.52-5.0513.3240.07532.5626581200819950.9980.07899.4
5.05-5.8413.9190.06834.4324817178417830.9980.07199.9
5.84-7.1513.470.06435.7720448151815180.9990.067100
7.15-10.1112.9630.04543.5215854122312230.9990.047100
10.11-44.4711.320.04242.1180947317150.9990.04397.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLF

2vlf


Resolution: 2.26→44.47 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1998 3.67 %
Rwork0.1833 52458 -
obs0.1847 54456 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.98 Å2 / Biso mean: 70.3409 Å2 / Biso min: 28.89 Å2
Refinement stepCycle: final / Resolution: 2.26→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7176 0 82 562 7820
Biso mean--80.58 74.18 -
Num. residues----907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4206X-RAY DIFFRACTION8.917TORSIONAL
12B4206X-RAY DIFFRACTION8.917TORSIONAL
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 (%)
2.2601-2.31660.38111410.349837513892100
2.3166-2.37920.34751420.310637253867100
2.3792-2.44920.32811430.299537273870100
2.4492-2.52820.33171420.275337283870100
2.5282-2.61860.30561440.246837713915100
2.6186-2.72340.25351430.221137533896100
2.7234-2.84740.23181430.200837763919100
2.8474-2.99740.23831430.183337623905100
2.9974-3.18520.19811440.171337633907100
3.1852-3.4310.22881440.163937813925100
3.431-3.77620.2221240.15593244336899
3.7762-4.32220.17421430.14683783392699
4.3222-5.4440.1881480.151738614009100
5.444-44.47860.20681540.184540334187100
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)
13.2555-1.2028-0.70874.078-1.04352.79150.01790.7020.0140.02450.32770.9066-0.2738-1.0815-0.17680.45710.0908-0.02790.78250.12660.4747-17.6612-54.7138-17.8622
25.84563.93970.34986.752-0.35447.53810.2089-0.2601-0.08840.4489-0.1698-0.3851-0.53920.2481-0.03590.35360.0609-0.01460.35240.01590.33134.8774-55.24642.0875
31.17050.1709-0.50822.6541-0.48322.51680.05180.07730.49810.185-0.0766-0.0917-1.12660.42760.01090.7905-0.1312-0.03020.56080.11190.56315.5562-34.8499-12.2489
41.45330.6726-1.241.4151-0.28222.08030.09920.39760.3613-0.12560.08340.0836-0.8105-0.09650.23040.6370.09080.03120.4470.10890.4387-5.2516-46.9937-19.7255
54.2493-0.93290.13341.0652-1.5712.72520.72460.51631.30710.1780.07780.0384-2.2064-1.4801-0.27791.27780.29940.24750.93560.35780.8633-19.1175-36.6212-22.2875
62.9364-1.94980.17585.6798-2.02644.38370.14470.85470.0097-0.78420.2170.67490.0601-0.3237-0.23620.4921-0.0192-0.03670.52470.1450.3874-13.2284-52.0032-27.0226
73.1426-0.387-2.7970.77310.44682.50010.15860.65211.243-0.14410.37371.1615-1.3661-2.22360.22691.29170.70120.3131.40560.54691.5125-27.3307-35.6196-20.13
83.09521.69031.03872.72060.89592.67520.0284-0.3213-0.07960.25430.1327-0.3244-0.15960.4081-0.1760.4382-0.00070.01480.5383-0.06170.35252.3445-59.066319.9155
91.66520.1016-0.42971.56110.52593.07940.1238-0.26690.52530.0895-0.04880.2929-0.7224-0.5054-0.01870.59660.15830.07310.5661-0.08420.5924-20.5105-41.870814.7074
103.85621.35390.99942.88971.29363.1773-0.011-0.51040.46470.165-0.0404-0.1359-0.49410.30840.00680.6173-0.04210.0480.5579-0.08230.3891.0759-48.4929.8565
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 285 )A89 - 285
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 361 )A286 - 361
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 401 )A362 - 401
6X-RAY DIFFRACTION6chain 'A' and (resid 402 through 430 )A402 - 430
7X-RAY DIFFRACTION7chain 'A' and (resid 431 through 456 )A431 - 456
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 57 )B2 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 311 )B58 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 456 )B312 - 456

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