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- PDB-5ted: Effector binding domain of QuiR in complex with shikimate -

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Basic information

Entry
Database: PDB / ID: 5ted
TitleEffector binding domain of QuiR in complex with shikimate
Components
  • His Tag peptide
  • Lmo0488 protein
KeywordsTRANSCRIPTION / LysR Type Transcriptional Regulator / LTTR / Shikimate
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-SKM / Lmo0488 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.889 Å
AuthorsPrezioso, S.M. / Christendat, D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-06747 Canada
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Shikimate Induced Transcriptional Activation of Protocatechuate Biosynthesis Genes by QuiR, a LysR-Type Transcriptional Regulator, in Listeria monocytogenes.
Authors: Prezioso, S.M. / Xue, K. / Leung, N. / Gray-Owen, S.D. / Christendat, D.
History
DepositionSep 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 2.0Mar 28, 2018Group: Data collection / Database references / Polymer sequence
Category: citation / citation_author / entity_poly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.pdbx_target_identifier
Revision 2.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lmo0488 protein
A: Lmo0488 protein
H: His Tag peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8705
Polymers52,5223
Non-polymers3482
Water8,935496
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-12 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 92.849, 113.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lmo0488 protein


Mass: 25852.334 Da / Num. of mol.: 2 / Fragment: UNP residues 89-297
Source method: isolated from a genetically manipulated source
Details: The mismatches are only in the structure due to the residue being disordered. The actual protein sequence does not have any mismatches to the database sequence.
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0488 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8Y9N7
#2: Protein/peptide His Tag peptide


Mass: 816.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.08 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M ammonium acetate pH 7.0, 14% w/v PEG3350, 5% glycerol, 25mM shikimate
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen Cryo Stream
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.889→20.765 Å / Num. obs: 40156 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 27
Reflection shellHighest resolution: 1.889 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.59 / Num. unique all: 3928 / Rsym value: 5.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000v0.95data collection
SCALEPACKdata scaling
PHASER1.1phasing
PDB_EXTRACT3.2data extraction
HKL-2000v0.95data reduction
PHENIX1.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Theoretical

Resolution: 1.889→20.765 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1827 4.72 %random
Rwork0.1765 ---
obs0.1787 38689 87.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.889→20.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 24 496 3902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073490
X-RAY DIFFRACTIONf_angle_d0.884732
X-RAY DIFFRACTIONf_dihedral_angle_d10.842062
X-RAY DIFFRACTIONf_chiral_restr0.06532
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.889-1.93970.23851010.23972144X-RAY DIFFRACTION68
1.9397-1.99670.28351260.23022439X-RAY DIFFRACTION77
1.9967-2.06110.26651270.22362591X-RAY DIFFRACTION81
2.0611-2.13470.26071340.19962685X-RAY DIFFRACTION84
2.1347-2.22010.26331370.20062779X-RAY DIFFRACTION86
2.2201-2.3210.2421410.18592763X-RAY DIFFRACTION86
2.321-2.44320.22421370.17832781X-RAY DIFFRACTION87
2.4432-2.5960.23871370.18982853X-RAY DIFFRACTION88
2.596-2.7960.24041470.18762971X-RAY DIFFRACTION92
2.796-3.07650.26061560.19553063X-RAY DIFFRACTION95
3.0765-3.51980.23261550.17443153X-RAY DIFFRACTION97
3.5198-4.42750.1781620.14673244X-RAY DIFFRACTION98
4.4275-20.76650.17281670.14383396X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.4526 Å / Origin y: 2.4653 Å / Origin z: 7.243 Å
111213212223313233
T0.1041 Å2-0.0016 Å20.038 Å2-0.1304 Å2-0.0484 Å2--0.1275 Å2
L0.5525 °20.3175 °20.04 °2-1.074 °2-0.4127 °2--0.6333 °2
S0.0071 Å °-0.0267 Å °0.0006 Å °-0.0261 Å °-0.0341 Å °0.0252 Å °0.0898 Å °-0.0294 Å °0.019 Å °
Refinement TLS groupSelection details: all

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