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- PDB-7tdl: M379A mutant tyrosine phenol-lyase complexed with 3-bromo-DL-phen... -

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Basic information

Entry
Database: PDB / ID: 7tdl
TitleM379A mutant tyrosine phenol-lyase complexed with 3-bromo-DL-phenylalanine
ComponentsTyrosine phenol-lyase
KeywordsLYASE / pyridoxal-5'-phosphate / mutation / substrate specificity
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-OY3 / PYRIDOXAL-5'-PHOSPHATE / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPhillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM137008 United States
CitationJournal: Chembiochem / Year: 2022
Title: M379A Mutant Tyrosine Phenol-lyase from Citrobacter freundii Has Altered Conformational Dynamics.
Authors: Phillips, R.S. / Jones, B. / Nash, S.
History
DepositionJan 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Tyrosine phenol-lyase
D: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,05820
Polymers205,7954
Non-polymers2,26316
Water27,5271528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21460 Å2
ΔGint-115 kcal/mol
Surface area54450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.250, 82.870, 94.330
Angle α, β, γ (deg.)113.160, 96.540, 102.210
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 51448.637 Da / Num. of mol.: 4 / Mutation: M379A
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 , 6 types, 1544 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-OY3 / (4Z)-4-({[(1E)-2-(3-bromophenyl)-1-carboxyethylidene]azaniumyl}methylidene)-2-methyl-5-[(phosphonooxy)methyl]-1,4-dihydropyridin-3-olate


Mass: 473.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H18BrN2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1528 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 mM PLP, 1 mM DTT, 19% PEG 5000MME

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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: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→58.41 Å / Num. obs: 213258 / % possible obs: 98.65 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.92 Å2 / CC1/2: 0.997 / Net I/σ(I): 6.48
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 21321 / CC1/2: 0.333

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC20211020data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLH

2vlh


Resolution: 1.6→58.41 Å / SU ML: 0.2452 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 1985 0.94 %
Rwork0.1774 209779 -
obs0.1778 211764 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14481 0 79 1529 16089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013715210
X-RAY DIFFRACTIONf_angle_d1.205420561
X-RAY DIFFRACTIONf_chiral_restr0.06512181
X-RAY DIFFRACTIONf_plane_restr0.01272690
X-RAY DIFFRACTIONf_dihedral_angle_d13.64385802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.35731340.355714213X-RAY DIFFRACTION93.39
1.64-1.680.38891400.333714809X-RAY DIFFRACTION97.53
1.68-1.730.32961410.310814823X-RAY DIFFRACTION97.86
1.73-1.790.29271410.286414953X-RAY DIFFRACTION98.4
1.79-1.850.35771410.26614892X-RAY DIFFRACTION97.72
1.85-1.930.30071440.243415143X-RAY DIFFRACTION99.75
1.93-2.020.28411430.229515102X-RAY DIFFRACTION99.66
2.02-2.120.30551430.21415107X-RAY DIFFRACTION99.49
2.12-2.260.24461430.199415128X-RAY DIFFRACTION99.34
2.26-2.430.26271420.191415068X-RAY DIFFRACTION99.28
2.43-2.670.22191430.183515087X-RAY DIFFRACTION99.42
2.67-3.060.24921430.168315145X-RAY DIFFRACTION99.68
3.06-3.860.17591430.138115143X-RAY DIFFRACTION99.78
3.86-58.410.14471440.126415166X-RAY DIFFRACTION99.85
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)
11.03170442771-0.408001750006-0.1472399488611.381357137390.1174372221371.29373427843-0.0279304695882-0.159526894634-0.06669996642490.135071825651-0.01603336731530.392651200646-0.0520721904849-0.3208841425610.002117911078240.1753022819080.01383352310620.03446418080510.29290478865-0.007365278226460.306870982324-26.036214924929.2779207987-14.0571509722
20.651628322678-0.05929530313850.2847507247241.50052742847-0.6600861911690.795201654888-0.0732264721127-0.110053519580.119840670090.5574419493530.00334167678794-0.211936755024-0.2487298495870.06745612322620.03359486547910.32583693869-0.00803441705736-0.0638117684020.236810754293-0.01496238041970.2461584871321.7978813172433.7888679391-6.90906004544
30.4903878852630.09718902702170.197016719591.177992532470.44546392590.6459132702550.02156376803660.01152445927040.03976789334590.107514643915-0.00801180028575-0.0863582030974-0.0710859229330.1090279648350.002094023228220.201490906235-0.0123465600588-0.005955705328430.2229951799230.01257398556250.22617921167-1.5595085815328.6354948701-15.2226942175
40.720014844799-0.111137723665-0.03249691148280.614872578074-0.6761499052070.739689709714-0.267488371664-0.3479583789090.4920628936210.7719676837560.298309291877-0.135946196305-0.2985265304920.03389788620730.07680566864010.4971833471990.117677422801-0.0673010263330.300497606363-0.1156908904940.352161313574-21.023769687441.7498424822-3.32179703926
50.7484013221280.4656951802170.1153023469230.678253013668-0.2700398531261.01457296636-0.531547907682-0.5231283329270.359017616230.9286082012490.3800958683210.5160400808940.4533393647760.0548542120797-0.1665896578070.7730559227620.3421070377210.1772665771180.480934419365-0.1258794857460.282933576282-28.099868807938.8386025442-2.48885860007
60.926930162645-0.4627404011480.4529554056760.968536606724-0.298034938860.99554197322-0.006839799643330.1525523311850.0441351650891-0.123636939281-0.085145111266-0.4539568090630.1529365000990.2733934995430.071860986380.3215467545890.0480139111330.03326565516190.2516459100480.02585612682110.3699151355460.960403762342-3.86436422688-16.7490977865
70.774155039662-0.0001636024027760.1001044994451.24775896751-0.5209385414780.8446801937460.0248072795604-0.290161609387-0.07273355797480.534834379015-0.02285453852920.09348558150420.0527083587825-0.0170179606679-0.00432856550220.510550435253-0.01951179073240.040072132210.3407540048030.01882814366790.211865929529-12.64364720561.901151627277.85383187547
80.7663299735910.02758170261370.05188409253580.583485999092-0.4237663258170.7443340406260.0136387389084-0.126818183074-0.05310816430680.3799258434220.0519397927860.1288048087690.0311626479265-0.08479453136-0.01670881710580.353014589643-0.01394320993550.02447885812780.2454180451810.01425622764560.205132527942-13.94240993493.36881190563-2.97579671233
91.28276882008-0.3216408698430.104745050280.977375776051-0.6727635485980.848718936942-0.0994011091542-0.1368233647060.2760604818250.246878171914-0.132491550168-0.7000497134760.1747041658960.3998097400480.07328744679520.4465016600270.063274301516-0.1221893291520.3677353021540.05094944567360.57255019438210.8637809399-6.59762323523-4.12584109696
100.2812919663640.1326511690650.1618267746570.528035701505-0.2510588633931.27869528685-0.06944223310260.1301218403020.0599653874377-0.134649117954-0.0473123214146-0.12851243093-0.150571888020.201827325670.04383473327250.223994199388-0.002531635240230.004268223486090.2650204261490.02195927788780.29961429613-18.186923125726.8705458399-40.8239736977
110.56553409112-0.051468517180.1963101338180.3913759435060.1310361263710.6188207552360.009863444004550.0142704351394-0.0358670823489-0.0490471642356-0.01084731167380.08249608078380.025773141063-0.1239402357830.006760216483440.167595606881-0.01096159047040.001905340505920.243695978882-0.00419553026420.247202048976-40.918946841413.3751129192-41.1161987823
120.801984932777-0.3340438839280.01584878921760.9057055117750.1700548993230.8847823050560.01047620185770.2370813349330.0465628257359-0.300073020532-0.0541318345767-0.058826969253-0.2006571402230.00876166146760.02297072667350.3320983764370.00669793044648-0.01453312819380.2661320072750.02476065234510.270520983218-26.746726101430.0908177679-53.7633211926
131.007517189020.5686779413020.4297535773861.028869114780.257336479020.5641252502080.123214763006-0.142811489162-0.05584942459770.312606978278-0.1114677649870.154701469150.249093793713-0.1228921149540.002854041139540.393287249446-0.02074223458950.02655139140050.2462393199880.01977149688510.305050140094-23.3706973347-12.9657589415-25.4538051621
140.546863002173-0.1811926336790.1407142846621.184454359520.3652635429670.8682273668560.02834411166180.109473811693-0.0778322541285-0.0880351116130.00336577337018-0.05758747869710.1405102529270.0719152967419-0.01785590856170.204694845270.01198087581780.009943361051940.213238781728-0.009147976126230.204754425499-11.7434379284-7.0774517555-48.3305412456
150.84395467649-0.226169056483-0.2122854824680.871145222254-0.01243454781130.5085546652760.004747304093460.144573905389-0.229980066538-0.0896809594158-0.008353381106110.2143792038980.314302968038-0.09510071322110.01826911800520.443225743181-0.03403452715-0.02935778922220.244616915564-0.02199270096830.339973351347-24.1529737535-23.8756134129-38.3588880721
160.84683137685-0.1632530129040.2504014273710.5472069861430.1327477154060.460354944224-0.061978447749-0.0275122537791-0.2318033479220.2404569070770.04458164329970.2319874581420.201531945331-0.1933194012160.02818342480480.489260441086-0.05208557571910.01151957763870.288700824886-0.0118000160040.397354772554-29.5122961905-23.4611466737-33.0759206591
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 57 )AA1 - 571 - 57
22chain 'A' and (resid 58 through 228 )AA58 - 22858 - 228
33chain 'A' and (resid 229 through 331 )AA229 - 331229 - 331
44chain 'A' and (resid 332 through 413 )AA332 - 413332 - 413
55chain 'A' and (resid 414 through 456 )AA414 - 456414 - 456
66chain 'B' and (resid 1 through 57 )BF1 - 571 - 57
77chain 'B' and (resid 58 through 271 )BF58 - 27158 - 271
88chain 'B' and (resid 272 through 332 )BF272 - 332272 - 332
99chain 'B' and (resid 333 through 456 )BF333 - 456333 - 456
1010chain 'C' and (resid 1 through 57 )CJ1 - 571 - 57
1111chain 'C' and (resid 58 through 331 )CJ58 - 33158 - 331
1212chain 'C' and (resid 332 through 456 )CJ332 - 456332 - 456
1313chain 'D' and (resid 1 through 57 )DN1 - 571 - 57
1414chain 'D' and (resid 58 through 331 )DN58 - 33158 - 331
1515chain 'D' and (resid 332 through 413 )DN332 - 413332 - 413
1616chain 'D' and (resid 414 through 456 )DN414 - 456414 - 456

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