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- PDB-6st6: Crystal Structure of Domain Swapped Trp Repressor V58I Variant -

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Basic information

Entry
Database: PDB / ID: 6st6
TitleCrystal Structure of Domain Swapped Trp Repressor V58I Variant
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 / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
Other privateDANSCATT Denmark
European Union (EU)UCPH-002 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_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: _citation.country / _citation.journal_abbrev ..._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.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _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 / _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.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _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_label_seq_id / _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)12,7547
Polymers12,3931
Non-polymers3616
Water93752
1
A: Trp operon repressor
hetero molecules

A: Trp operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,50814
Polymers24,7862
Non-polymers72112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area3750 Å2
ΔGint-10 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.260, 85.260, 115.320
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

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Components

#1: Protein Trp operon repressor


Mass: 12393.188 Da / Num. of mol.: 1 / Mutation: V58I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: P0A881
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.07 Å3/Da / Density % sol: 75.76 %
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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→45.45 Å / Num. obs: 16145 / % possible obs: 99.88 % / Redundancy: 44.04 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.077 / Net I/σ(I): 34.59
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.2623 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1570 / CC1/2: 0.81 / Rrim(I) all: 0.2652 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MI7

1mi7


Resolution: 2.05→39.99 Å / SU ML: 0.2782 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.0722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3106 806 5 %
Rwork0.277 15319 -
obs0.2786 16125 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.35 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 24 52 920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019874
X-RAY DIFFRACTIONf_angle_d0.41331174
X-RAY DIFFRACTIONf_chiral_restr0.0304131
X-RAY DIFFRACTIONf_plane_restr0.0033151
X-RAY DIFFRACTIONf_dihedral_angle_d28.2906333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.180.39461310.37912483X-RAY DIFFRACTION99.81
2.18-2.350.36741300.35792487X-RAY DIFFRACTION99.96
2.35-2.580.40011330.33662518X-RAY DIFFRACTION99.96
2.58-2.960.33521330.32472526X-RAY DIFFRACTION99.92
2.96-3.720.3171360.28142574X-RAY DIFFRACTION99.96
3.72-39.990.27521430.23922731X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -27.5934478753 Å / Origin y: 29.6891299714 Å / Origin z: 17.1701278311 Å
111213212223313233
T0.385780916563 Å20.0832051717924 Å20.0789132632141 Å2-0.619956313305 Å20.199622874151 Å2--0.485417007844 Å2
L0.472504402698 °20.582273421314 °2-1.00672428593 °2-0.354489220057 °20.263536769895 °2--0.212123681767 °2
S0.057777326271 Å °0.107968297352 Å °0.484859456057 Å °-0.283404026308 Å °-0.0322964585248 Å °0.0685885826809 Å °0.194941494382 Å °-0.06210751631 Å °0.113693041102 Å °
Refinement TLS groupSelection details: all

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