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

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Basic information

Entry
Database: PDB / ID: 6dvx
TitleCitrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-phenylalanine
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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...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 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-P70 / Chem-P71 / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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
DepositionJun 25, 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
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)104,0597
Polymers102,8652
Non-polymers1,1935
Water8,881493
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)208,11714
Polymers205,7314
Non-polymers2,38610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area20530 Å2
ΔGint-84 kcal/mol
Surface area56010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.780, 132.670, 144.970
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 - 92
141(chain A and (resid 2 through 65 or resid 67...A94 - 289
151(chain A and (resid 2 through 65 or resid 67...A291 - 380
161(chain A and (resid 2 through 65 or resid 67...A382 - 1458
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 - 92
241(chain B and (resid 2 through 65 or resid 67...B94 - 289
251(chain B and (resid 2 through 65 or resid 67...B2 - 1501
261(chain B and (resid 2 through 65 or resid 67...B2 - 1501
271(chain B and (resid 2 through 65 or resid 67...B382 - 387
281(chain B and (resid 2 through 65 or resid 67...B392 - 1457

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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) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 5 types, 498 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P71 / (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-phenylpropanoic acid


Mass: 394.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2O7P
#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: Chemical ChemComp-P70 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-phenylalanine


Mass: 394.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M triethanolamine-HCl, 0.5 mM pyridoxal-5'-phosphate, 1 mM EDTA, 5 mM 2-mercaptoethanol, 36-40% PEG 5000 MME
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→37.752 Å / Num. obs: 54151 / % possible obs: 99.8 % / Redundancy: 27.743 % / Biso Wilson estimate: 54.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.16 / Χ2: 1.072 / Net I/σ(I): 17.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.27-2.3315.0153.9740.8839510.3674.11299.9
2.33-2.3920.1823.3421.2238730.5653.42899.9
2.39-2.4630.0592.7731.8337090.7782.8299.7
2.46-2.5430.0692.252.3536350.8882.28899.8
2.54-2.6230.0321.7353.0735340.8941.76599.6
2.62-2.7130.0231.4433.7634270.9221.46899.8
2.71-2.8230.051.0744.9732860.9641.09399.7
2.82-2.9329.9860.7866.6531820.9770.899.7
2.93-3.0629.9890.5788.7630500.9860.58899.9
3.06-3.2129.920.41411.5729310.9930.42199.8
3.21-3.3829.7620.27416.4928100.9970.279100
3.38-3.5929.5590.18822.3826420.9980.19199.9
3.59-3.8429.3660.12130.9724980.9990.123100
3.84-4.1429.0480.0940.38234110.091100
4.14-4.5428.9620.06649.4216010.067100
4.54-5.0828.4520.06153.9197010.062100
5.08-5.8628.2570.0655.42175210.061100
5.86-7.1827.7510.05558.78150310.056100
7.18-10.1526.9610.03972.6119110.04100
10.15-37.75223.6150.03670.670610.03798.1

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Processing

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

2vlh


Resolution: 2.27→37.752 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.01
RfactorNum. reflection% reflection
Rfree0.2188 1997 3.7 %
Rwork0.1857 --
obs0.187 54040 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 200.73 Å2 / Biso mean: 79.2741 Å2 / Biso min: 38.67 Å2
Refinement stepCycle: final / Resolution: 2.27→37.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 78 496 7736
Biso mean--85.43 78.39 -
Num. residues----906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4261X-RAY DIFFRACTION10.466TORSIONAL
12B4261X-RAY DIFFRACTION10.466TORSIONAL
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 (%)
2.2701-2.32680.43251400.406836593799100
2.3268-2.38980.38071420.369737003842100
2.3898-2.46010.35441390.33613629376899
2.4601-2.53940.36611410.310736603801100
2.5394-2.63020.33511410.270636683809100
2.6302-2.73550.28061410.250936803821100
2.7355-2.85990.28781420.225136963838100
2.8599-3.01060.26521410.203236783819100
3.0106-3.19920.25791430.187837013844100
3.1992-3.4460.20951420.178737043846100
3.446-3.79250.20341430.153437403883100
3.7925-4.34060.15961440.138737513895100
4.3406-5.46610.16961460.145138083954100
5.4661-37.75710.20031520.173739694121100
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)
15.246-1.91130.77565.43031.78815.248-0.08480.6108-0.18430.10730.488-0.75540.34751.4197-0.39440.74020.02590.02250.8093-0.13020.4652-42.081-11.7887-17.7821
22.38012.23720.30673.95531.29883.64110.2033-0.25590.07750.522-0.2630.13980.3247-0.21840.03860.82240.03860.02340.5019-0.02750.4671-64.3416-10.65132.506
31.49670.31350.33622.65550.29552.5980.07890.1548-0.49720.0573-0.0173-0.04820.8223-0.2975-0.07911.099-0.0786-0.00520.5527-0.09820.6513-64.2067-34.1849-14.0257
42.9413-0.08260.53942.64710.1482.46970.1781-0.0701-0.30880.2211-0.21970.34510.7914-0.37620.08930.8948-0.10420.03430.5664-0.11210.5015-67.8913-24.2855-6.889
51.57290.57890.7460.85660.69173.96950.05910.3929-0.4235-0.02370.1681-0.17660.75220.4895-0.08291.04710.1038-0.02810.5562-0.10610.5605-50.9983-20.4779-20.3672
62.3187-0.35750.83922.3737-1.23891.02490.04330.3998-0.4145-0.26760.2412-0.65810.7480.6729-0.05161.08540.1134-0.00270.5752-0.1530.5714-45.9509-21.4946-25.2311
71.1788-0.49270.67465.54123.44862.98430.17230.3422-0.58560.87840.7089-1.3131.49221.7972-1.24791.57330.7902-0.29851.7194-0.61461.2974-33.0024-30.4195-20.4407
85.74762.4024-1.58823.3825-1.16882.0577-0.0302-0.21720.1460.2060.17470.3620.1815-0.4189-0.14560.8210.0087-0.00930.590.04310.4162-62.1051-7.219719.9104
91.5754-0.01210.29772.0191-0.60483.08810.0924-0.1911-0.46850.1049-0.0621-0.25770.66160.4618-0.00910.84150.1101-0.05960.54930.0570.5922-38.9595-25.460815.8973
101.9335-0.3627-0.88841.11660.34953.8538-0.0291-0.2605-0.09890.099-0.1308-0.0540.20030.42640.17460.84040.0253-0.07910.48250.0520.4864-44.1481-10.767316.0909
112.9531.4876-0.69893.8281-1.33753.13240.0241-0.4693-0.38320.1492-0.04980.20660.644-0.4470.00841.0249-0.0752-0.01630.67150.08640.5326-63.3391-19.72229.8398
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 87 )A58 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 228 )A88 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 285 )A229 - 285
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 386 )A286 - 386
6X-RAY DIFFRACTION6chain 'A' and (resid 387 through 429 )A387 - 429
7X-RAY DIFFRACTION7chain 'A' and (resid 430 through 456 )A430 - 456
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 57 )B2 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 285 )B58 - 285
10X-RAY DIFFRACTION10chain 'B' and (resid 286 through 331 )B286 - 331
11X-RAY DIFFRACTION11chain 'B' and (resid 332 through 456 )B332 - 456

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