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- PDB-6chk: Crystal structure of LacI family transcriptional regulator from L... -

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Basic information

Entry
Database: PDB / ID: 6chk
TitleCrystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound TRIS
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION / Transcriptional Regulator / Lactobacillus casei / Structural Genomics
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I ...Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesLactobacillus paracasei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPatskovsky, Y. / Toro, R. / Shabalin, I.G. / Kowiel, M. / Porebski, P.J. / Minor, W. / Jaskolski, M. / Bhosle, R. / Al Obaidi, N. / Chamala, S. ...Patskovsky, Y. / Toro, R. / Shabalin, I.G. / Kowiel, M. / Porebski, P.J. / Minor, W. / Jaskolski, M. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative, E.F.I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG008424 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117325 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117080 United States
CitationJournal: Bioinformatics / Year: 2019
Title: Automatic recognition of ligands in electron density by machine learning.
Authors: Kowiel, M. / Brzezinski, D. / Porebski, P.J. / Shabalin, I.G. / Jaskolski, M. / Minor, W.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 7, 2018ID: 4RK3
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6834
Polymers30,5031
Non-polymers1813
Water5,675315
1
A: Transcriptional regulator, LacI family
hetero molecules

A: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3668
Polymers61,0052
Non-polymers3616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area3990 Å2
ΔGint-38 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.715, 108.715, 125.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-281-

PHE

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Components

#1: Protein Transcriptional regulator, LacI family


Mass: 30502.631 Da / Num. of mol.: 1 / Fragment: UNP residues 54-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus paracasei (bacteria)
Strain: ATCC 334 / BCRC 17002 / CIP 107868 / KCTC 3260 / NRRL B-441
Gene: LSEI_2103 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q036L9
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.17 M sodium acetate, 0.085 M Tris-HCl, pH 8.5, 25.5% w/v PEG4000, 15% w/v ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.17 M sodium acetate, 0.085 M Tris-HCl, pH 8.5, 25.5% w/v PEG4000, 15% w/v glycerol, cryoprotectant = reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26573 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 30.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
SHELXphasing
SHELXmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.677 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 775 2.9 %RANDOM
Rwork0.1438 ---
obs0.1453 25794 99.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 108.18 Å2 / Biso mean: 31.106 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---3.76 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 10 315 2387
Biso mean--30.03 41.54 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192165
X-RAY DIFFRACTIONr_bond_other_d0.0020.022037
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9572954
X-RAY DIFFRACTIONr_angle_other_deg0.9934717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61724.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4441515
X-RAY DIFFRACTIONr_chiral_restr0.10.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 36 -
Rwork0.224 1903 -
all-1939 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 6.551 Å / Origin y: 24.333 Å / Origin z: 17.594 Å
111213212223313233
T0.0891 Å2-0.0143 Å20.0165 Å2-0.1199 Å20.003 Å2--0.0146 Å2
L1.0454 °2-0.764 °20.4052 °2-1.4808 °2-0.4812 °2--0.7018 °2
S0.033 Å °0.0449 Å °-0.0978 Å °0.0033 Å °0.0051 Å °0.0861 Å °0.0204 Å °-0.0681 Å °-0.038 Å °

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