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- PDB-6st7: Crystal Structure of Domain Swapped Trp Repressor V58I Variant wi... -

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Basic information

Entry
Database: PDB / ID: 6st7
TitleCrystal Structure of Domain Swapped Trp Repressor V58I Variant with bound L-trp
ComponentsTrp operon repressor
KeywordsDNA BINDING PROTEIN / HOSTAL / L-trp binding / Domain swapping
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / TRYPTOPHAN / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSprenger, J. / Lawson, C.L. / Carey, J. / Drouard, F. / von Wachenfeldt, C. / Schulz, A. / Linse, S. / Lo Leggio, L.
Funding support Denmark, Sweden, United States, 6items
OrganizationGrant numberCountry
Other privateVillum Experiment grant 17535 Denmark
European Union (EU)MAX4ESSFUN grant LU001 Sweden
National Science Foundation (NSF, United States)DBI13-58737 United States
National Science Foundation (NSF, United States)DBI16-59726 United States
European Union (EU)UCPH-002 Denmark
Other privateDANSCATT Denmark
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of L-tryptophan.
Authors: Sprenger, J. / Lawson, C.L. / von Wachenfeldt, C. / Lo Leggio, L. / Carey, J.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 2.0Jul 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_starting_model / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _software.version / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: During the review process we were made aware of that the first residue (methionine) is present in the density which we did not model in the first submitted structure. We now have completed ...Details: During the review process we were made aware of that the first residue (methionine) is present in the density which we did not model in the first submitted structure. We now have completed the model with the additional N-terminal methionine. Please also note that in the previous submission it looked like the assembly was annotated as dimer, but it should be monomar (as PDB ID 1mi7) Then, the sequence we first provided is missing 2 residues in the N-terminus that originate from the protease cleavage of the purification tag. We uploaded the correct sequence, however, we want to make sure that the first residue in the PDB file is Met 1 Thank you very much and let me know if there are nay further questions. Kind regards, Janina Sprenger
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4713
Polymers12,2071
Non-polymers2642
Water36020
1
A: Trp operon repressor
hetero molecules

A: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9436
Polymers24,4142
Non-polymers5294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area3030 Å2
ΔGint-21 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.830, 86.830, 114.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

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Components

#1: Protein Trp operon repressor


Mass: 12206.979 Da / Num. of mol.: 1 / Mutation: V58I
Source method: isolated from a genetically manipulated source
Details: The actual sequence is that from the Uniprot entry P0A881 but with V58I mutation
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P0A881
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 5.15 Å3/Da / Density % sol: 76.11 % / Description: bi-pyramidal, hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Na HEPES, 100 mM sodium chloride, 27.5-35%(v/v) isopropanol, pH 7.5
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.45→45.57 Å / Num. obs: 9881 / % possible obs: 99.9 % / Redundancy: 10.49 % / Biso Wilson estimate: 81.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0627 / Rrim(I) all: 0.0658 / Net I/σ(I): 17.52
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.2095 / Num. unique obs: 1543 / CC1/2: 0.434 / Rrim(I) all: 0.2198 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ST6

6st6


Resolution: 2.45→43.41 Å / SU ML: 0.4127 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.8651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2868 493 5 %
Rwork0.2544 9373 -
obs0.2561 9866 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.33 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 19 20 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018875
X-RAY DIFFRACTIONf_angle_d0.38751181
X-RAY DIFFRACTIONf_chiral_restr0.0316132
X-RAY DIFFRACTIONf_plane_restr0.0032153
X-RAY DIFFRACTIONf_dihedral_angle_d28.1377336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.70.4071190.36032269X-RAY DIFFRACTION99.62
2.7-3.090.36291210.33252288X-RAY DIFFRACTION99.75
3.09-3.890.32921220.27812335X-RAY DIFFRACTION99.96
3.89-43.410.25351310.22712481X-RAY DIFFRACTION99.77
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)
14.290771467271.38379495055-1.035497985793.049886992210.1251151003456.39459841331-0.60362569-0.63812092434-0.6575113023590.619357248669-0.0900814983119-0.3717249020021.24266782802-0.4769619086320.6175490055460.87987274634-0.05078512394390.1099389644010.672850995293-0.03633897641070.683686815945-44.484259024315.440219742-5.7436501027
24.548920863685.047334227615.691396717843.493469723325.751818575334.92767315608-0.8532338037850.1976306358750.587335276907-0.6359675607610.2922255860130.380745939579-0.9658111544620.4428402021940.6579692134211.21908332087-0.161821533469-0.2418027203790.9660396155870.02211550871050.884003535663-27.780118375744.93946332313.04415147322
34.042027464951.02542795486-2.226331393685.46313670487-3.281031078274.950174919710.642286623377-0.8114529924420.5697438733221.41312889289-0.165651857064-0.853285937959-0.7767913685871.33577319799-0.3792465228710.9256587403150.0187615582497-0.3164880021730.883649625052-0.2472987531710.9453165802671.9953927367766.294317379920.4438728432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 105 )

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