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- PDB-3jy6: Crystal structure of LacI Transcriptional regulator from Lactobac... -

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Basic information

Entry
Database: PDB / ID: 3jy6
TitleCrystal structure of LacI Transcriptional regulator from Lactobacillus brevis
ComponentsTranscriptional regulator, LacI family
KeywordsTranscription regulator / NYSGXRC / PSI-II / transcriptional regulator / Lac I / Protein structure Initiative / 11238g / structural genomics / New York SGX Research Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / 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 brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsSyed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of LacI Transcriptional regulator from Lactobacillus brevis
Authors: Syed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4337
Polymers124,2734
Non-polymers1603
Water3,171176
1
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)62,1362
Polymers62,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-13 kcal/mol
Surface area21350 Å2
MethodPISA
2
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2965
Polymers62,1362
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-10 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.570, 109.328, 113.342
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulator, LacI family


Mass: 31068.234 Da / Num. of mol.: 4 / Fragment: sequence database residues 64-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / Gene: LVIS_0444 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q03T70
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 0.2M Mg Cl2, 0.1M Bis Tris, 25% Peg 3350, 2M NaCl, Ethylene Glycol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2009 / Details: MIRRORS
RadiationMonochromator: SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 65400 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.9 / % possible all: 80.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→40.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 81982.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3111 5 %RANDOM
Rwork0.247 ---
obs0.247 61427 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.81 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.183 Å20 Å2-0.914 Å2
2--1.57 Å20 Å2
3---1.612 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.97→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8106 0 9 176 8291
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.982.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 271 5.2 %
Rwork0.301 4898 -
obs--44.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EDO.PAREDO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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