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- PDB-8v9p: Proteus vulgaris tryptophan indole-lyase complexed with (3S)-diox... -

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Basic information

Entry
Database: PDB / ID: 8v9p
TitleProteus vulgaris tryptophan indole-lyase complexed with (3S)-dioxindolyl-L-alanine
ComponentsTryptophanase
KeywordsLYASE / pyridoxal-5'-phosphate / fold I / tetramer
Function / homology
Function and homology information


tryptophanase activity / tryptophanase
Similarity search - Function
Tryptophanase / 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-YQK / Tryptophanase
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPhillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: Acs Catalysis / Year: 2024
Title: Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism.
Authors: Phillips, R.S. / Brown, S.M. / Patel, R.S.
History
DepositionDec 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophanase
B: Tryptophanase
C: Tryptophanase
D: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,33213
Polymers210,2364
Non-polymers2,0969
Water20,2851126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-78 kcal/mol
Surface area55530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.342, 112.717, 119.518
Angle α, β, γ (deg.)90.000, 97.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Tryptophanase / L-tryptophan indole-lyase / TNase


Mass: 52558.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: tnaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28796, tryptophanase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#3: Chemical
ChemComp-YQK / (2~{E})-2-[(~{Z})-[2-methyl-3-oxidanyl-5-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]-1~{H}-pyridin-4-ylidene]methyl]imino-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-1~{H}-indol-3-yl]propanoic acid


Mass: 465.351 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H20N3O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium phosphate, pH 8.0, 1 mM DTT, 0.1 mM PLP, 22% PEG 4000, 0.2 M CsCl

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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: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.845→61.87 Å / Num. obs: 76925 / % possible obs: 91.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.03 Å2 / CC1/2: 0.98 / Net I/σ(I): 5.1
Reflection shellResolution: 1.845→1.87 Å / Num. unique obs: 3846 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
autoPROCdata processing
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→61.87 Å / SU ML: 0.2489 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 3856 5.02 %
Rwork0.199 72990 -
obs0.2014 76846 50.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.36 Å2
Refinement stepCycle: LAST / Resolution: 1.85→61.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14816 0 72 1128 16016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003515422
X-RAY DIFFRACTIONf_angle_d0.611520885
X-RAY DIFFRACTIONf_chiral_restr0.04582230
X-RAY DIFFRACTIONf_plane_restr0.00482726
X-RAY DIFFRACTIONf_dihedral_angle_d12.70835791
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)
10.254646757465-0.168765294701-0.1153557031290.30812096546-0.09790394919670.222320118055-0.00657448926952-0.056832052610.1441759082930.1827527180880.0201537420143-0.0916004894433-0.07946572883370.06108019649950.03423902438650.0590967416511-0.08383296335070.02374703035180.00714679605467-0.04399969852110.038220657449711.556924030224.44053119229.0399102547
20.7277740381010.157715044652-0.08458968456741.0792489913-0.2421986381710.2115619417360.04463998467480.08434366890830.158023441585-0.02082167974190.00868678752485-0.0816768650547-0.130513269604-0.0304434653741-0.01603344591370.1622774800270.0006831215691140.05063911477340.03981858415460.05166573559080.17068274195511.485333040445.536819344815.1666820172
30.2570926207140.0224300329813-0.0815995776570.217595933544-0.06488342825450.3257919990410.02751785400930.08769016116890.1911934337010.0702649758367-0.02491599773650.12142752491-0.192448297711-0.1514906914510.05399911705160.03782304069880.04842671540540.03997301677570.03900506263210.03468430514210.1278019986483.2379695336835.686363366317.7200567905
40.9420748390140.01792111399540.6112849512040.573751406630.0759988843960.483107978271-0.05894733212070.04017492579610.388800636899-0.0115466148260.0318404960783-0.255900697084-0.3117681273060.1105033315860.04974179912540.305659797395-0.0438455215640.06847206008930.0603997466848-0.03612709521670.24376789363614.571145075544.791819270735.6915514815
50.738071281172-0.307701457983-0.155642268480.256276489514-0.1901252858470.542884826920.0269581823195-0.2297039132170.389488937720.1316539787420.00434951470702-0.254885810368-0.4233042865540.275106633571-0.1005438389790.407285642395-0.09332677032040.06190409127790.187409493705-0.08469174810990.30801139266420.709251884942.785519816140.5795460336
60.239052746362-0.05328313468740.09547962997670.303936304329-0.003098072751140.125074346285-0.0004729728945980.1125736549220.00383969854192-0.0293577634084-0.0868756393049-0.002971494459570.00479642427844-0.020257609072-0.1052428271590.0670321813129-0.0267511091386-0.05675691272460.0754075075855-0.04086782969820.045367391227321.807627199810.089742418316.3279982128
71.059686588110.0426535016425-0.6515547413460.00963614063175-0.09993797419741.082977046120.016242206977-0.03465814184450.2567392627360.000629545394754-0.0405866899499-0.0326615902746-0.1199258748820.195123655012-0.05813685787130.0555676263681-0.007415524125530.02429711380780.1188390036060.09687452603180.25129941953238.573675954631.44773169219.34295027119
82.0923703791-0.6830396156-0.5386126138060.6973562259980.3278218146220.5297663328630.04808642410520.211956481389-0.0296212530292-0.0853219790658-0.118643634627-0.05551826509620.0102299848992-0.0163272573490.07137404914040.06943958440680.03837037985580.05551284257710.205170605510.1020576613880.20062468871838.111328908523.18570873611.26707543694
90.2420994321860.01388864302230.04718885086530.03869212721720.06370434252220.1093204510060.02928732341620.0285216753440.0672237468734-0.001133273165230.0246232972492-0.226805745278-0.0359935022810.1049918912860.0767272273438-0.0697010895004-0.0617181665944-0.008463027581310.07941858551590.04354550777860.30603553097542.866740454217.788520367713.2340108865
100.3338137831560.06146248073830.06290113303190.1693441229510.1168780874530.1763874829780.01097052397-0.00643860408406-0.06124922250060.003159649426020.00775894815928-0.07520265701440.009175900745370.0316240447662-0.03421620417260.010312534463-0.0267650208819-0.02211556038750.02400115642860.01807975061920.082568296224729.66386562887.1320103545217.3555178077
110.603088378094-0.00223684705675-0.3532716102730.2221137958290.1745393107020.3419279402670.155543627320.2985208051370.203776999264-0.235822140798-0.0639660013776-0.080057276255-0.203104159631-0.13363562285-0.1426658546130.2262949741350.06164448873180.155473931170.1676449884460.02794585969760.16892331357732.64555211685.96729950864-7.02721574399
120.6685423490.4637326329190.1955807916641.05602032257-0.2332432255981.536707361-0.007775293010380.3257115394270.273733559141-0.3111214885930.00322243469618-0.145805737571-0.2190553879130.0874065902997-0.03110897427230.1536437001230.04190533892820.0916158725350.1602263170910.06869567766970.18955877669126.729918282811.263937548-2.88481628657
130.53999488636-0.0944763470606-0.0954376931981.335466412460.2881364426110.0725530142060.1093941048820.3790128076970.0571645250308-0.561183603441-0.100026682567-0.0666914724059-0.149339257112-0.109207757273-0.09752443336180.2992640589550.04714115839520.1023366021660.247770255317-0.01214579296250.14554598152521.33959758028.58869813096-7.17892921307
140.3025034544510.00311053147119-0.07859559971050.564961555729-0.03245094056970.5789397403610.0569758017193-0.04299707294880.04288364542310.000395143317108-0.006039693124260.09848054757830.0143461059617-0.1045360915380.02184817240760.0941346644728-0.0486667892649-0.02679510717840.0452765384281-0.02286898487610.03278596086972.946225395466.2085949191842.738049564
151.387787474340.326101600593-0.3640716619780.302169980903-0.7245605462921.90762774185-0.0483737199474-0.306944419977-0.258710948991-0.06402898093780.0293130769001-0.006810204939130.4061879988250.08576647325310.05392126035310.317693479041-0.03285686087310.08528472264070.162484470430.04786337914120.1135568545121.87965861132-15.490755007460.7985903477
160.122672039966-0.02689185324560.05176230394690.156788544352-0.1545602582570.4958789067760.0204518966678-0.0818752760514-0.04237970230790.03153955344340.03640603073470.02722167290010.114703154591-0.1011724586470.06881532702320.335502582884-0.06448996269120.0720005092330.2361578524390.02482759806590.0490306708239-2.91955062754-4.5012050873168.2879023013
170.130503123883-0.00921119346137-0.03589141139280.1022652612120.01090063336270.222500228740.0328505854377-0.134143563866-0.01208906744180.216342563882-0.00037120113011-0.04850656112290.0528728606590.0786791246393-0.0565264354040.258858876802-0.0652745922718-0.03750257799960.107067725993-0.0147192959321-0.02187921855178.950875831121.7495640630857.3695349958
180.251107168101-0.1415895267210.2182834606510.1482937764730.005082488949060.438021130535-0.0479792732416-0.115866781444-0.112476676730.1730681775120.004794194392360.1639638127080.185742839888-0.196682977820.176234198810.286429205021-0.003227194944010.1482098672060.104868815058-0.02179967456710.0886727442204-13.48450906219.007578678755.1573455095
190.7264117750180.8811983358310.6190659617793.887442536971.985722087971.43297847372-0.0295123133822-0.1761011929820.1617446417940.0371827597269-0.03098264531380.67075231551-0.12728463814-0.4541217907790.09445041211660.3156784685460.01342392917560.1694858470160.3043446946460.03670717343770.331575046641-22.90030744681.9131786445650.4027640214
200.4467981306020.193751901705-0.1990787522320.4411132993860.2258926047120.5371975301160.00957576259565-0.0593191563123-0.03554638556810.1138278516320.0379392933689-0.1148206820510.159696129630.0653323739428-0.05290402975490.0774842264132-0.0470340178214-0.03360261001070.0279890610126-0.005755953098420.065276068895711.6020375049-8.3963091233228.8282266117
210.429079832714-0.4850848661820.4605830393011.76920361961-0.0005663886376150.716297584191-0.0342918178764-0.035121522356-0.0870034591160.1534022035930.03160418385020.163921508460.0849541221495-0.179134551866-0.01762992112290.235156557068-0.06576843251180.03006374898460.0833779337917-0.002358251824010.0659727779075-7.66871409001-26.221342984439.0698584516
220.2042389936440.164837937097-0.07982544601150.256444756041-0.1267488564840.1275099218620.0309523925264-0.0518219396082-0.05045974014820.0988688577821-0.0397665268321-0.01224569909830.0599007256371-0.04011198197790.041940341960.281384639906-0.1015456175190.05868684773830.054227951821-0.008730946504080.0960876113889-0.999290748455-33.661661094428.7893477584
23-0.001870916547050.005610352847330.0038010626440.0883064861410.1389220535390.232327076393-0.03173769593830.0751213345788-0.0816343044066-0.01609852229060.0505414211871-0.03222076441810.148354169737-0.0808986780350.1338801660380.129755229102-0.1369519473130.00913446952999-0.0210133318667-0.136500450653-0.000315537877127-1.02418642173-17.144940335223.5353169852
241.46716874513-0.1439845109150.6679188569460.0967140192533-0.1495176624220.3868340074310.0205058685154-0.24040511342-0.4960736474980.4391028406580.08139771043490.01778191808720.394107196174-0.0694839776271-0.01698092456910.459999536019-0.005871420541050.06472176993370.09709608355730.004358421282230.25330271500618.3899597888-28.826974475429.3735771831
251.047412989720.413471596086-0.5648176253571.12743224097-0.2104886150292.25263987305-0.0741838282602-0.314102612647-0.4632223214610.4069362246970.0300489302897-0.2382931376550.6275727142080.4479786362860.1002368426060.4542991875170.1050780093840.0229878956780.246144927160.02703892162610.36187184826725.4336080461-26.993090076133.0724273649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 99 )AA2 - 991 - 98
22chain 'A' and (resid 100 through 168 )AA100 - 16899 - 167
33chain 'A' and (resid 169 through 341 )AA169 - 341168 - 340
44chain 'A' and (resid 342 through 423 )AA342 - 423341 - 422
55chain 'A' and (resid 424 through 467 )AA424 - 467423 - 466
66chain 'B' and (resid 2 through 99 )BE2 - 991 - 98
77chain 'B' and (resid 100 through 132 )BE100 - 13299 - 131
88chain 'B' and (resid 133 through 155 )BE133 - 155132 - 154
99chain 'B' and (resid 156 through 295 )BE156 - 295155 - 294
1010chain 'B' and (resid 296 through 342 )BE296 - 342295 - 341
1111chain 'B' and (resid 343 through 371 )BE343 - 371342 - 370
1212chain 'B' and (resid 372 through 423 )BE372 - 423371 - 422
1313chain 'B' and (resid 424 through 467 )BE424 - 467423 - 466
1414chain 'C' and (resid 2 through 99 )CG2 - 991 - 98
1515chain 'C' and (resid 100 through 132 )CG100 - 13299 - 131
1616chain 'C' and (resid 133 through 190 )CG133 - 190132 - 189
1717chain 'C' and (resid 191 through 342 )CG191 - 342190 - 341
1818chain 'C' and (resid 343 through 437 )CG343 - 437342 - 436
1919chain 'C' and (resid 438 through 467 )CG438 - 467437 - 466
2020chain 'D' and (resid 2 through 99 )DK2 - 991 - 98
2121chain 'D' and (resid 100 through 132 )DK100 - 13299 - 131
2222chain 'D' and (resid 133 through 190 )DK133 - 190132 - 189
2323chain 'D' and (resid 191 through 342 )DK191 - 342190 - 341
2424chain 'D' and (resid 343 through 423 )DK343 - 423342 - 422
2525chain 'D' and (resid 424 through 467 )DK424 - 467423 - 466

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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