7OS9 | pdb_00007os9

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

• PDB DOI: https://doi.org/10.2210/pdb7OS9/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-08 Released: 2021-07-14 
• Deposition Author(s): Sprenger, J., Lawson, C.L., Lo Leggio, L., Von Wachenfeldt, C., Carey, J.
• Funding Organization(s): National Science Foundation (NSF, United States), Other private, European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.279 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

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

• PubMed: 34196612 
• DOI: https://doi.org/10.1107/S2053230X21006142
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
Department of Biology, Lund University, SE-221 00 Lund, Sweden.
Chemistry Department, Princeton University, Princeton, NJ 08544, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.98 kDa 
• Atom Count: 879 
• Modeled Residue Count: 108 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trp operon repressor	A [auth AA]	131	Escherichia coli	Mutation(s): 0  Gene Names:  trpR, A6581_18385, A6V01_04405, A8C65_14935, A9819_24995, A9R57_08265, A9X72_21335, AC789_1c48680, ACN002_4668, ACN68_21430, ACN81_09780, ACU57_07675, ACU90_07280, AM270_09365, AM464_16695, AMK83_27270, AML35_20440, ARC77_19250, AU473_26900, AUQ13_08415, AUS26_22800, AW059_08865, AWB10_21955, B7C53_17175, BB545_14420, BHF03_15595, BHS81_26165, BHS87_24520, BIZ41_21215, BJJ90_22270, BK248_20485, BK292_12740, BK296_03460, BMA87_10415, BMT91_18370, BN17_44101, BOH76_24290, BON63_20360, BON65_08470, BON69_07095, BON72_08435, BON75_00780, BON76_14530, BON94_26195, BON95_07735, BON98_11485, BTQ04_23975, BTQ06_24870, BUE81_16670, BVL39_03110, BW690_00300, BWP17_03400, BZL31_17540, C2U48_10565, C5F72_22700, C5F73_07005, C5N07_17095, C5P01_07990, C5P44_08275, C6669_05245, C7235_21160, C7B02_11800, C7B06_04925, C7B07_05220, C9114_21605, C9160_22560, C9201_20530, C9306_03555, C9E25_18335, C9E67_26175, C9Z03_09790, C9Z28_19770, C9Z37_20800, C9Z70_09005, CA593_03805, CDC27_23720, CG692_08005, CI641_015615, CI693_18930, CI694_23760, CJU64_26420, CO706_22135, COD30_03045, COD46_20790, CR538_21575, CR539_03945, CRD98_11815, CRE06_01130, CRM83_16015, CV83915_01578, CVH05_08745, CWS33_04590, D0X26_18810, D2184_09510, D2185_16920, D3821_23135, D3C88_12015, D3O91_16665, D3Y67_17480, D4011_01135, D4023_22040, D4074_00750, D4660_01140, D4L91_01140, D4M06_02415, D4U85_03305, D5H35_24540, D5I97_01140, D6004_23555, D6C36_01125, D6D43_01140, D6T60_11970, D6X63_08995, D6X76_13520, D7K33_04340, D7K63_01095, D7K66_00440, D7Z75_16480, D8Y65_02820, D9610_23095, D9C99_15895, D9D20_19820, D9D44_07685, D9E35_19630, D9E73_03395, D9F87_18115, D9G69_16600, D9G95_07020, D9H68_15935, D9H70_05845, D9H94_13515, D9I18_11175, D9I87_14765, D9I97_13025, D9J11_11390, D9J44_25325, D9J52_08700, D9J60_02975, D9K48_08570, D9K54_15845, D9L89_01085, D9X77_00725, D9X97_01085, D9Z28_18610, DAH18_06235, DAH23_12170, DAH30_08095, DAH34_19280, DAH37_09580, DEN89_11195, DEO04_18305, DEO20_17795, DIV22_05325, DJ503_01195, DL455_02585, DL530_08550, DL545_21350, DL800_30245, DLT82_04670, DLU82_21005, DLX40_19555, DM155_24370, DM962_04215, DMI04_01140, DMI53_02480, DMO02_01135, DMZ30_06755, DN627_19110, DN660_13525, DN703_01935, DN808_14480, DNB37_02400, DNC98_17460, DND79_18095, DNI21_17215, DNJ62_01115, DNK12_01140, DNQ45_19280, DNR41_14180, DOE35_01135, DOS18_02625, DOT59_24265, DOT81_01135, DOU81_01135, DOY22_01140, DOY56_01140, DOY61_23025, DOY67_10275, DP258_19105, DP277_20165, DQF57_06895, DQG35_01140, DQO13_17735, DQP61_21260, DRP48_01140, DRW19_17750, DS143_25375, DS721_01135, DS732_04835, DT034_21690, DTL43_03435, DU333_06890, DXT69_19285, DXT73_20105, DXX80_016240, E0I42_00080, E2119_12980, E2127_21690, E2128_12850, E2129_16080, E2134_17300, E2135_21990, E2148_13160, E4K53_18690, E4K55_18560, E4K60_12230, E4K61_18790, E5P24_13755, E5P28_12505, E5S34_02000, E5S38_08455, E5S42_10445, E5S44_06140, E5S56_23145, EA184_04275, EA213_16860, EA225_04700, EAI42_33745, EAI46_33920, EAI52_14880, EAM59_07640, EAN77_19710, EAX79_01780, EB509_09660, EB510_06435, EB515_01070, EB525_RS16045, EBJ06_00130, EBM08_22860, EBP16_19345, EC1094V2_3867, EC382_07625, ECs5351, ED225_13115, ED600_13105, ED607_14570, ED611_13370, ED903_11830, ED944_01070, EEA45_15965, EEP23_10995, EF082_20360, EF173_01070, EG599_11930, EG808_15810, EGU87_01070, EH412_06720, EHD63_01070, EHD79_05080, EHH55_17860, EHJ36_10540, EHJ66_00130, EHV81_21300, EHV90_04840, EHW09_03955, EHX09_01070, EI021_05235, EI032_10995, EI041_04065, EIA21_01075, EJC75_21825, EKI52_11425, EL79_3878, EL80_3823, ELT49_20540, ELY05_14215, EO241_17865, EPS91_19875, EPS94_21705, EPT01_16115, EQ825_04225, EXM29_16655, EXX06_07905, EXX13_04410, EXX23_12930, EXX24_16280, EXX53_09955, EXX55_07370, EXX71_18980, EXX87_02425, EYD11_19445, EYV18_08240, EYY27_03825, EYY78_17540, F0L67_10010, F1E19_12390, F6T51_19540, F6V70_09385, F7F23_01740, F7F26_10325, F7F56_01035, F7G03_00560, F9X20_008395, F9X20_08465, FE846_01340, FORC82_4055, FQ021_21755, FQ915_25030, FRV13_28075, FTV90_08225, FTV92_14250, FV250_07230, FV293_11830, FV438_05725, FWK02_10545, FY127_17485, G5603_21475, G5608_20945, G5632_15105, G5668_03085, G5670_02890, G5680_03455, G5688_03350, G5696_00385, G6Z99_20925, G9448_11000, G9P49_18905, G9P50_18100, GE400_12575, GHD50_13790, GIJ01_04455, GIY19_12035, GJD97_23890, GKF39_00290, GKF74_00805, GKF86_00290, GKF89_12930, GKG12_14550, GNX12_20200, GNZ02_13510, GNZ05_10690, GP650_16080, GP662_19085, GP666_05955, GP698_01030, GP720_10495, GP935_08970, GP945_22470, GP946_22210, GP954_15325, GQA06_20595, GQE22_01750, GQE33_14685, GQE34_05160, GQE42_01600, GQE64_18250, GQE87_00150, GQF59_17505, GQM04_10245, GQM06_25835, GQM09_09945, GQM10_01805, GQM13_11745, GQM17_15405, GQM18_04870, GQM28_17840, GQN24_16590, GRW02_19230, GRW30_15100, GRW57_28435, GRW80_18065, GRW81_15230, GUB85_09010, GUB91_10980, GUB95_10820, GUC01_14755, GUC12_12120, H4P50_21530, H4P51_21380, H5C68_19175, HCR07_13850, HF065_001611, HF523_08125, HFD31_000981, HFD39_001216, HFD59_001394, HFD69_001001, HFU80_004715, HGS12_19830, HGS82_21670, HGT58_01030, HH707_003924, HH830_003655, HHH24_000627, HHJ44_20195, HI083_003572, HIA56_004124, HIN76_000160, HIO03_003674, HIQ74_004742, HIQ82_000938, HIT59_003429, HIZ44_002801, HIZ62_001017, HJI76_004374, HJI79_001730, HJM41_002453, HJO53_002211, HJQ03_001127, HJR60_003165, HJR92_001670, HJS53_000987, HJV81_004219, HKA14_000989, HKA45_001389, HKA57_004351, HKC58_004381, HL601_06790, HLQ75_23670, HLQ92_06100, HLT96_09810, HLU13_12935, HMG20_16175, HMG24_05635, HMG27_04810, HMG35_06040, HMQ05_08145, HMT01_21910, HNC40_00080, HNC80_05030, HNC88_23010, HNC94_14400, HND23_04230, HNN86_19045, HNO03_08750, HNO08_09030, HNV44_11685, HP431_09980, HS093_10640, HV005_18215, HV021_19240, HV022_20340, HV065_21670, HV068_20415, HV109_20260, HV149_20360, HV168_11510, HV188_03370, HV226_01725, HV244_18725, HVV38_12855, HVV53_20305, HVV70_02670, HVV78_03160, HVW09_02610, HVW11_06855, HVW37_21080, HVW43_12675, HVW45_19870, HVW59_10900, HVW60_19385, HVW76_19095, HVW95_12140, HVW98_03005, HVX22_19635, HVX24_19230, HVX30_03025, HVX33_10820, HVX51_20590, HVX60_11630, HVX69_20905, HVX73_20165, HVX96_11010, HVY01_19865, HVY77_22110, HVY79_03195, HVY93_20095, HVZ24_19370, HVZ42_20415, HVZ44_19985, HVZ53_20905, HVZ62_11145, HVZ71_21305, HW43_03625, HWQ66_01755, HX136_21525, HXS78_19380, HZT35_13805, IEM32_05095, PGD_03638, PU06_28270, RG28_04820, RK56_013995, TUM18780_37810, WQ89_19785
UniProt
Find proteins for C3SE17 (Escherichia coli) Explore C3SE17  Go to UniProtKB:  C3SE17

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	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 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.747	α = 90
b = 85.747	β = 90
c = 115.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Sprenger, J., Lawson, C.L., Lo Leggio, L., Von Wachenfeldt, C., Carey, J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DBI13-58737
National Science Foundation (NSF, United States)	United States	DBI16-59726
Other private	Denmark	Villum Experiment grant 17535
European Union (EU)	Sweden	MAX4ESSFUN grant LU001
Other private	Denmark	DANSCATT
European Union (EU)	Denmark	UCPH-002

Revision History  

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