7OS9

Crystal Structure of Domain Swapped Trp Repressor V58I Variant with purification tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan.

Sprenger, J.Lawson, C.L.von Wachenfeldt, C.Lo Leggio, L.Carey, J.

(2021) Acta Crystallogr F Struct Biol Commun 77: 215-225

  • DOI: https://doi.org/10.1107/S2053230X21006142
  • Primary Citation of Related Structures:  
    6ST6, 6ST7, 7OS9

  • PubMed Abstract: 

    The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand L-tryptophan (L-Trp) indicate that L-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with L-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it bears a disordered extension of about 20 residues, is accessible in the large solvent channels of the domain-swapped crystal form, as in the structures reported previously in this form for TrpR without N-terminal extensions. These findings inspire the exploration of L-Trp analogs and N-terminal modifications as labels to orient guest proteins that cannot otherwise be crystallized in the solvent channels of crystalline domain-swapped TrpR hosts for potential diffraction analysis.


  • Organizational Affiliation

    Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trp operon repressorA [auth AA]131Escherichia coliMutation(s): 0 
Gene Names: 
trpRA6581_18385A6V01_04405A8C65_14935A9819_24995A9R57_08265A9X72_21335AC789_1c48680ACN002_4668ACN68_21430ACN81_09780ACU57_07675ACU90_07280AM270_09365AM464_16695AMK83_27270AML35_20440ARC77_19250AU473_26900AUQ13_08415AUS26_22800AW059_08865AWB10_21955B7C53_17175BB545_14420BHF03_15595BHS81_26165BHS87_24520BIZ41_21215BJJ90_22270BK248_20485BK292_12740BK296_03460BMA87_10415BMT91_18370BN17_44101BOH76_24290BON63_20360BON65_08470BON69_07095BON72_08435BON75_00780BON76_14530BON94_26195BON95_07735BON98_11485BTQ04_23975BTQ06_24870BUE81_16670BVL39_03110BW690_00300BWP17_03400BZL31_17540C2U48_10565C5F72_22700C5F73_07005C5N07_17095C5P01_07990C5P44_08275C6669_05245C7235_21160C7B02_11800C7B06_04925C7B07_05220C9114_21605C9160_22560C9201_20530C9306_03555C9E25_18335C9E67_26175C9Z03_09790C9Z28_19770C9Z37_20800C9Z70_09005CA593_03805CDC27_23720CG692_08005CI641_015615CI693_18930CI694_23760CJU64_26420CO706_22135COD30_03045COD46_20790CR538_21575CR539_03945CRD98_11815CRE06_01130CRM83_16015CV83915_01578CVH05_08745CWS33_04590D0X26_18810D2184_09510D2185_16920D3821_23135D3C88_12015D3O91_16665D3Y67_17480D4011_01135D4023_22040D4074_00750D4660_01140D4L91_01140D4M06_02415D4U85_03305D5H35_24540D5I97_01140D6004_23555D6C36_01125D6D43_01140D6T60_11970D6X63_08995D6X76_13520D7K33_04340D7K63_01095D7K66_00440D7Z75_16480D8Y65_02820D9610_23095D9C99_15895D9D20_19820D9D44_07685D9E35_19630D9E73_03395D9F87_18115D9G69_16600D9G95_07020D9H68_15935D9H70_05845D9H94_13515D9I18_11175D9I87_14765D9I97_13025D9J11_11390D9J44_25325D9J52_08700D9J60_02975D9K48_08570D9K54_15845D9L89_01085D9X77_00725D9X97_01085D9Z28_18610DAH18_06235DAH23_12170DAH30_08095DAH34_19280DAH37_09580DEN89_11195DEO04_18305DEO20_17795DIV22_05325DJ503_01195DL455_02585DL530_08550DL545_21350DL800_30245DLT82_04670DLU82_21005DLX40_19555DM155_24370DM962_04215DMI04_01140DMI53_02480DMO02_01135DMZ30_06755DN627_19110DN660_13525DN703_01935DN808_14480DNB37_02400DNC98_17460DND79_18095DNI21_17215DNJ62_01115DNK12_01140DNQ45_19280DNR41_14180DOE35_01135DOS18_02625DOT59_24265DOT81_01135DOU81_01135DOY22_01140DOY56_01140DOY61_23025DOY67_10275DP258_19105DP277_20165DQF57_06895DQG35_01140DQO13_17735DQP61_21260DRP48_01140DRW19_17750DS143_25375DS721_01135DS732_04835DT034_21690DTL43_03435DU333_06890DXT69_19285DXT73_20105DXX80_016240E0I42_00080E2119_12980E2127_21690E2128_12850E2129_16080E2134_17300E2135_21990E2148_13160E4K53_18690E4K55_18560E4K60_12230E4K61_18790E5P24_13755E5P28_12505E5S34_02000E5S38_08455E5S42_10445E5S44_06140E5S56_23145EA184_04275EA213_16860EA225_04700EAI42_33745EAI46_33920EAI52_14880EAM59_07640EAN77_19710EAX79_01780EB509_09660EB510_06435EB515_01070EB525_RS16045EBJ06_00130EBM08_22860EBP16_19345EC1094V2_3867EC382_07625ECs5351ED225_13115ED600_13105ED607_14570ED611_13370ED903_11830ED944_01070EEA45_15965EEP23_10995EF082_20360EF173_01070EG599_11930EG808_15810EGU87_01070EH412_06720EHD63_01070EHD79_05080EHH55_17860EHJ36_10540EHJ66_00130EHV81_21300EHV90_04840EHW09_03955EHX09_01070EI021_05235EI032_10995EI041_04065EIA21_01075EJC75_21825EKI52_11425EL79_3878EL80_3823ELT49_20540ELY05_14215EO241_17865EPS91_19875EPS94_21705EPT01_16115EQ825_04225EXM29_16655EXX06_07905EXX13_04410EXX23_12930EXX24_16280EXX53_09955EXX55_07370EXX71_18980EXX87_02425EYD11_19445EYV18_08240EYY27_03825EYY78_17540F0L67_10010F1E19_12390F6T51_19540F6V70_09385F7F23_01740F7F26_10325F7F56_01035F7G03_00560F9X20_008395F9X20_08465FE846_01340FORC82_4055FQ021_21755FQ915_25030FRV13_28075FTV90_08225FTV92_14250FV250_07230FV293_11830FV438_05725FWK02_10545FY127_17485G5603_21475G5608_20945G5632_15105G5668_03085G5670_02890G5680_03455G5688_03350G5696_00385G6Z99_20925G9448_11000G9P49_18905G9P50_18100GE400_12575GHD50_13790GIJ01_04455GIY19_12035GJD97_23890GKF39_00290GKF74_00805GKF86_00290GKF89_12930GKG12_14550GNX12_20200GNZ02_13510GNZ05_10690GP650_16080GP662_19085GP666_05955GP698_01030GP720_10495GP935_08970GP945_22470GP946_22210GP954_15325GQA06_20595GQE22_01750GQE33_14685GQE34_05160GQE42_01600GQE64_18250GQE87_00150GQF59_17505GQM04_10245GQM06_25835GQM09_09945GQM10_01805GQM13_11745GQM17_15405GQM18_04870GQM28_17840GQN24_16590GRW02_19230GRW30_15100GRW57_28435GRW80_18065GRW81_15230GUB85_09010GUB91_10980GUB95_10820GUC01_14755GUC12_12120H4P50_21530H4P51_21380H5C68_19175HCR07_13850HF065_001611HF523_08125HFD31_000981HFD39_001216HFD59_001394HFD69_001001HFU80_004715HGS12_19830HGS82_21670HGT58_01030HH707_003924HH830_003655HHH24_000627HHJ44_20195HI083_003572HIA56_004124HIN76_000160HIO03_003674HIQ74_004742HIQ82_000938HIT59_003429HIZ44_002801HIZ62_001017HJI76_004374HJI79_001730HJM41_002453HJO53_002211HJQ03_001127HJR60_003165HJR92_001670HJS53_000987HJV81_004219HKA14_000989HKA45_001389HKA57_004351HKC58_004381HL601_06790HLQ75_23670HLQ92_06100HLT96_09810HLU13_12935HMG20_16175HMG24_05635HMG27_04810HMG35_06040HMQ05_08145HMT01_21910HNC40_00080HNC80_05030HNC88_23010HNC94_14400HND23_04230HNN86_19045HNO03_08750HNO08_09030HNV44_11685HP431_09980HS093_10640HV005_18215HV021_19240HV022_20340HV065_21670HV068_20415HV109_20260HV149_20360HV168_11510HV188_03370HV226_01725HV244_18725HVV38_12855HVV53_20305HVV70_02670HVV78_03160HVW09_02610HVW11_06855HVW37_21080HVW43_12675HVW45_19870HVW59_10900HVW60_19385HVW76_19095HVW95_12140HVW98_03005HVX22_19635HVX24_19230HVX30_03025HVX33_10820HVX51_20590HVX60_11630HVX69_20905HVX73_20165HVX96_11010HVY01_19865HVY77_22110HVY79_03195HVY93_20095HVZ24_19370HVZ42_20415HVZ44_19985HVZ53_20905HVZ62_11145HVZ71_21305HW43_03625HWQ66_01755HX136_21525HXS78_19380HZT35_13805IEM32_05095PGD_03638PU06_28270RG28_04820RK56_013995TUM18780_37810WQ89_19785

UniProt
Find proteins for C3SE17 (Escherichia coli)
Explore C3SE17 
Go to UniProtKB:  C3SE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3SE17
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth AA]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.747α = 90
b = 85.747β = 90
c = 115.56γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDBI13-58737
National Science Foundation (NSF, United States)United StatesDBI16-59726
Other privateDenmarkVillum Experiment grant 17535
European Union (EU)SwedenMAX4ESSFUN grant LU001
Other privateDenmarkDANSCATT
European Union (EU)DenmarkUCPH-002

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description