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- PDB-4rkr: Crystal structure of LacI family transcriptional regulator from A... -

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Basic information

Entry
Database: PDB / ID: 4rkr
TitleCrystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007, complex with lactose
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / lactose
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
alpha-lactose / Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of LacI Transcriptional Regulator PurR from Arthrobacter Sp, Target Nysgxrc 11027R
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. / Burley, S.K. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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 / chem_comp ...atom_site / 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 / 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_atom_id / _atom_site.label_comp_id / _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.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / chem_comp / citation_author
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID
Revision 2.2Sep 20, 2023Group: 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: 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)125,2858
Polymers123,9164
Non-polymers1,3694
Water8,035446
1
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6424
Polymers61,9582
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-10 kcal/mol
Surface area21760 Å2
MethodPISA
2
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6424
Polymers61,9582
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-12 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.936, 124.912, 117.043
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 500
2114B0 - 500
3114C0 - 500
4114D0 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.963497, 0.014512, 0.267326), (0.023865, -0.989899, 0.139753), (0.266654, 0.141031, 0.953418)68.59874, 40.47886, -12.44951
3given(0.920036, -0.006071, -0.391788), (-0.005948, -0.999981, 0.001527), (-0.391789, 0.000925, -0.920054)14.9385, 69.99606, 72.46032
4given(-0.992405, -0.022322, 0.120972), (-0.039093, 0.989648, -0.13809), (-0.116638, -0.14177, -0.983004)76.05155, -17.80325, 70.0656

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Components

#1: Protein
Transcriptional regulator, LacI family


Mass: 30978.941 Da / Num. of mol.: 4 / Fragment: UNP Residues 59-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: FB24 / Gene: Arth_3918 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0K1X3
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.16 Å3/Da / Density % sol: 43.51 %
Crystal growpH: 6.5
Details: Protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:HAOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir plus 20 mM lactose; ...Details: Protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:HAOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir plus 20 mM lactose; 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 315 / Detector: CCD / Date: Jul 10, 2014 / Details: MIRRORS
RadiationMonochromator: ROCK CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52910 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RKQ

4rkq


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.846 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25183 1588 3 %RANDOM
Rwork0.17142 ---
obs0.17387 51293 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.889 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å2-0 Å2-2.3 Å2
2--0.29 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 92 446 8494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198198
X-RAY DIFFRACTIONr_bond_other_d0.0010.027925
X-RAY DIFFRACTIONr_angle_refined_deg1.21.98511147
X-RAY DIFFRACTIONr_angle_other_deg0.71318192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85251079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04323.374326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661568
X-RAY DIFFRACTIONr_chiral_restr0.0620.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021755
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_it12.5796.9134328
X-RAY DIFFRACTIONr_mcbond_other12.5896.9114327
X-RAY DIFFRACTIONr_mcangle_it12.34110.7945400
X-RAY DIFFRACTIONr_mcangle_other12.34310.7975401
X-RAY DIFFRACTIONr_scbond_it20.9718.2323870
X-RAY DIFFRACTIONr_scbond_other20.9718.2323870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other20.17912.2625747
X-RAY DIFFRACTIONr_long_range_B_refined18.72430.0999322
X-RAY DIFFRACTIONr_long_range_B_other18.72430.0999322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3844 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.340.5
2BMEDIUM POSITIONAL0.370.5
3CMEDIUM POSITIONAL0.320.5
4DMEDIUM POSITIONAL0.410.5
1AMEDIUM THERMAL9.3710
2BMEDIUM THERMAL8.9510
3CMEDIUM THERMAL8.9810
4DMEDIUM THERMAL10.610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 106 -
Rwork0.291 3640 -
obs--95.85 %

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