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- PDB-6dxv: Citrobacter freundii tyrosine phenol-lyase F448A mutant -

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Basic information

Entry
Database: PDB / ID: 6dxv
TitleCitrobacter freundii tyrosine phenol-lyase F448A mutant
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
: / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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
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)103,1374
Polymers103,0592
Non-polymers782
Water8,431468
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)206,2758
Polymers206,1184
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area18670 Å2
ΔGint-80 kcal/mol
Surface area56450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.350, 132.180, 145.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 78 or resid 80 through 456))
21(chain B and (resid 2 through 78 or resid 80 through 387 or resid 395 through 456))

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
11ASNASNTYRTYR(chain A and (resid 2 through 78 or resid 80 through 456))AA2 - 781 - 77
12LEULEUILEILE(chain A and (resid 2 through 78 or resid 80 through 456))AA80 - 45679 - 455
21ASNASNTYRTYR(chain B and (resid 2 through 78 or resid 80 through 387 or resid 395 through 456))BB2 - 781 - 77
22LEULEUGLYGLY(chain B and (resid 2 through 78 or resid 80 through 387 or resid 395 through 456))BB80 - 38779 - 386
23HISHISILEILE(chain B and (resid 2 through 78 or resid 80 through 387 or resid 395 through 456))BB395 - 456394 - 455

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Components

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


Mass: 51529.578 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 BL21(DE3) (bacteria) / 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 / Mutation: F448A / Source method: obtained synthetically / Formula: K / References: tyrosine phenol-lyase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: MARMOSAIC 300 mm CCD / 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: 2.2→37.48 Å / Num. obs: 58142 / % possible obs: 96.23 % / Redundancy: 6 % / Biso Wilson estimate: 47.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1218 / Rpim(I) all: 0.05459 / Rrim(I) all: 0.1338 / Net I/σ(I): 7.14
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6 % / Rmerge(I) obs: 4.86 / Num. unique obs: 5733 / CC1/2: 0.469 / Rpim(I) all: 2.174 / Rrim(I) all: 5.334 / % possible all: 75.46

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Processing

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

2tpl


Resolution: 2.2→37.479 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1950 3.45 %
Rwork0.208 54613 -
obs0.2095 56563 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.37 Å2 / Biso mean: 90.946 Å2 / Biso min: 35.34 Å2
Refinement stepCycle: final / Resolution: 2.2→37.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 2 468 7642
Biso mean--69.82 90.38 -
Num. residues----903
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4231X-RAY DIFFRACTION9.339TORSIONAL
12B4231X-RAY DIFFRACTION9.339TORSIONAL
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 (%)
2.2001-2.25510.67351070.69852980308775
2.2551-2.3160.60131280.57453570369889
2.316-2.38420.37271420.376239984140100
2.3842-2.46110.38921420.34213976411899
2.4611-2.54910.35281410.31873946408798
2.5491-2.65110.34271420.28443964410699
2.6511-2.77170.28831420.250540114153100
2.7717-2.91780.27841440.211840284172100
2.9178-3.10050.23061440.186940284172100
3.1005-3.33980.20511440.17514038418299
3.3398-3.67560.24761440.161640514195100
3.6756-4.20690.20091420.16523989413198
4.2069-5.29780.18681340.15613742387690
5.2978-37.48470.23591540.18554292444699
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)
12.8162-1.26470.36865.0581-2.7453.31560.19910.90010.3597-0.360.36480.7513-0.465-1.2376-0.39480.70080.1944-0.03540.93160.13940.502441.693911.6431-17.7638
26.10064.1646-0.52766.6941-1.72759.24840.3448-0.3301-0.02510.205-0.4053-0.4239-0.42780.52190.0020.57820.077-0.02040.5150.02510.447564.112310.88212.4865
31.56080.22030.24633.4532-0.80743.12220.01650.21290.73760.1927-0.0950.1011-1.33380.20880.06961.2293-0.0917-0.01860.690.21790.858163.647434.3776-13.9945
43.2230.0405-0.17222.0636-0.95844.1775-0.02060.18450.53670.1495-0.0002-0.0518-0.74330.23740.1640.81220.02020.05020.45710.11670.573859.608921.6299-14.2594
54.0169-0.42131.10655.5105-1.0543.32930.14690.44630.9063-0.13370.24571.1246-1.2169-1.62-0.3031.08770.36280.1131.03570.35230.915339.712524.1877-23.3176
62.03511.15790.95723.86311.42744.94150.1461-0.2452-0.05490.46370.1177-0.5478-0.16440.562-0.23510.7223-0.06340.03890.5756-0.06230.402561.79787.046119.9232
72.5456-0.135-0.61122.5851.29743.07630.2787-0.33480.86430.0601-0.14140.2232-0.85-0.3454-0.07640.93910.08760.17210.6766-0.13190.803739.099524.563314.8974
84.79691.84391.10333.42631.23944.4308-0.0845-0.61520.56760.2195-0.0687-0.1155-0.85130.47320.09750.8916-0.09320.03770.6666-0.13820.474860.707117.592129.8708
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 361 )A229 - 361
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 456 )A362 - 456
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 57 )B2 - 57
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 311 )B58 - 311
8X-RAY DIFFRACTION8chain 'B' and (resid 312 through 456 )B312 - 456

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