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- PDB-4rk5: Crystal structure of LacI family transcriptional regulator from L... -

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Basic information

Entry
Database: PDB / ID: 4rk5
TitleCrystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound sucrose
ComponentsTranscriptional regulator, LacI familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / sucrose
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
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
sucrose / ACETATE ION / Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesLactobacillus casei ATCC 334 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.35 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / 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 (EFI)
CitationJournal: To be Published
Title: Crystal Structure of LacI Transcriptional Regulator Lsei_2103 from Lactobacillus casei, Target EFI-512911
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3364
Polymers30,9121
Non-polymers4243
Water4,918273
1
A: Transcriptional regulator, LacI family
hetero molecules

A: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6738
Polymers61,8242
Non-polymers8496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area5160 Å2
ΔGint-17 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.754, 108.754, 125.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / Transcriptional regulation


Mass: 30912.123 Da / Num. of mol.: 1 / Fragment: UNP residues 54-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei ATCC 334 (bacteria)
Gene: LSEI_2103 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q036L9
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% glycerol, cryoprotectant = reservoir + 100 mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
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: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 62512 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 39
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.88 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.35→44.1 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.397 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS (CG, CD1, CD2, CE1, CE2, CZ) OF RESIDUE A PHE 281 ARE ON A SPECIAL POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.14093 1865 3 %RANDOM
Rwork0.10905 ---
obs0.11003 60647 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.35→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 28 273 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192271
X-RAY DIFFRACTIONr_bond_other_d0.0020.022182
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9663117
X-RAY DIFFRACTIONr_angle_other_deg1.64835016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69324.112107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1541515
X-RAY DIFFRACTIONr_chiral_restr0.1210.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212647
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.193.1841135
X-RAY DIFFRACTIONr_mcbond_other6.1893.1831133
X-RAY DIFFRACTIONr_mcangle_it6.3075.3771425
X-RAY DIFFRACTIONr_mcangle_other6.3055.3761426
X-RAY DIFFRACTIONr_scbond_it10.5833.9431130
X-RAY DIFFRACTIONr_scbond_other10.583.9451131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.9696.3061672
X-RAY DIFFRACTIONr_long_range_B_refined8.71412.9792713
X-RAY DIFFRACTIONr_long_range_B_other8.71312.982714
X-RAY DIFFRACTIONr_rigid_bond_restr634442
X-RAY DIFFRACTIONr_sphericity_free34.803571
X-RAY DIFFRACTIONr_sphericity_bonded20.35454596
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 129 -
Rwork0.197 4406 -
obs--99.54 %

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