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- PDB-6mo3: Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydro... -

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Basic information

Entry
Database: PDB / ID: 6mo3
TitleCitrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from L-serine
Components(Tyrosine phenol- ...) x 2
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 / : / SERINE / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 4, 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_conn_type
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.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
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)104,35710
Polymers103,2462
Non-polymers1,1118
Water11,440635
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)208,71420
Polymers206,4914
Non-polymers2,22216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area20570 Å2
ΔGint-68 kcal/mol
Surface area55030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.680, 133.810, 143.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Tyrosine phenol- ... , 2 types, 2 molecules AB

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


Mass: 51508.754 Da / Num. of mol.: 1
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
#2: Protein Tyrosine phenol-lyase / Beta-tyrosinase


Mass: 51736.871 Da / Num. of mol.: 1
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 , 6 types, 643 molecules

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


Mass: 95.099 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H5NO / References: tryptophanase
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H13N2O7P / References: tryptophanase
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.73 Å3/Da / Density % sol: 54.99 %
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: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→55.12 Å / Num. obs: 109170 / % possible obs: 99.9 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.1531 / Net I/σ(I): 15.62
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 15.3 % / Rmerge(I) obs: 3.295 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLF

2vlf


Resolution: 1.79→55.12 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 1993 1.83 %
Rwork0.159 --
obs0.16 109100 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.8 Å2
Refinement stepCycle: LAST / Resolution: 1.79→55.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 0 73 635 7931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83470.35851430.33817509X-RAY DIFFRACTION100
1.8347-1.88430.29351410.29267591X-RAY DIFFRACTION100
1.8843-1.93980.26871250.26667538X-RAY DIFFRACTION100
1.9398-2.00240.24251500.22477578X-RAY DIFFRACTION100
2.0024-2.0740.22781300.20147588X-RAY DIFFRACTION100
2.074-2.1570.22991600.18267561X-RAY DIFFRACTION100
2.157-2.25520.21191350.16547624X-RAY DIFFRACTION100
2.2552-2.37410.19121410.1587583X-RAY DIFFRACTION100
2.3741-2.52280.19241370.1567649X-RAY DIFFRACTION100
2.5228-2.71760.16771500.15017673X-RAY DIFFRACTION100
2.7176-2.99110.17621360.14927672X-RAY DIFFRACTION100
2.9911-3.42380.16751450.14587695X-RAY DIFFRACTION100
3.4238-4.31340.17111470.12687779X-RAY DIFFRACTION100
4.3134-55.14640.14721530.15258067X-RAY DIFFRACTION100
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)
12.2543-1.33360.56432.7155-0.53851.418-0.00790.0746-0.0345-0.13690.14210.5174-0.1039-0.6331-0.09710.22560.0298-0.01230.44140.06770.27539.094513.7225-17.58
22.15441.2749-0.9642.5152-0.96836.2620.0955-0.14320.09150.2079-0.1207-0.2134-0.28210.41430.04050.17050.0209-0.00790.22960.01040.264334.550511.11592.2911
30.77230.1965-0.15631.2168-0.36621.90070.0850.06610.28250.0776-0.0706-0.0934-0.54170.2613-0.01360.3471-0.05790.03220.30750.04460.366434.194928.3511-11.9907
42.5034-0.3559-0.27511.2927-0.52362.01420.09760.27120.7797-0.00490.12730.2255-0.8195-0.4917-0.07930.53450.14780.03350.44910.150.500710.445927.7204-23.9681
52.29811.29490.90172.32360.85191.89620.0622-0.079-0.10280.15890.1138-0.3604-0.02360.3571-0.1740.2267-0.0028-0.00730.3102-0.03750.232932.46396.643820.0856
60.71820.0464-0.21841.24890.45191.78470.0902-0.15040.27580.0279-0.0910.1938-0.5101-0.31970.00520.33310.09760.03580.3393-0.06750.36759.333624.222315.0238
72.21450.7670.36961.88920.90392.19870.008-0.22240.30360.18920.0675-0.1666-0.26760.2694-0.0780.3188-0.019-0.00030.3058-0.06510.252631.195417.461129.8885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 57 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 58 THROUGH 88 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 89 THROUGH 331 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 332 THROUGH 456 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 2 THROUGH 57 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 58 THROUGH 311 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 312 THROUGH 456 )

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