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

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Basic information

Entry
Database: PDB / ID: 4rkq
TitleCrystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor
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
Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.903 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 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 28, 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

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)124,25911
Polymers123,9164
Non-polymers3437
Water11,169620
1
A: Transcriptional regulator, LacI family
B: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1777
Polymers61,9582
Non-polymers2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-33 kcal/mol
Surface area22490 Å2
MethodPISA
2
C: Transcriptional regulator, LacI family
D: Transcriptional regulator, LacI family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0824
Polymers61,9582
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-9 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.244, 125.126, 116.422
Angle α, β, γ (deg.)90.00, 96.68, 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(-0.966619, 0.015182, 0.255766), (0.02189, -0.989699, 0.141478), (0.255279, 0.142354, 0.95633)69.17578, 40.46803, -12.13459
3given(0.91868, 0.005927, -0.394957), (0.0066, -0.999978, 0.000346), (-0.394946, -0.002925, -0.9187)14.51649, 69.59684, 72.55789
4given(-0.990007, -0.031776, 0.13739), (-0.050748, 0.989288, -0.136874), (-0.131569, -0.142479, -0.981015)75.96573, -17.51547, 70.45312

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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: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.17 Å3/Da / Density % sol: 43.53 %
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:NaOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir; vapor diffusion, ...Details: protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:NaOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir; vapor diffusion, sitting drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2014 / Details: MIRRORS
RadiationMonochromator: ROCK CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 82386 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.63 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.903→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.439 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20704 2439 3 %RANDOM
Rwork0.15436 ---
obs0.15591 79909 99.33 %-
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: 29.492 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-1.13 Å2
2---0.23 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.903→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8008 0 19 620 8647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198198
X-RAY DIFFRACTIONr_bond_other_d0.0010.027953
X-RAY DIFFRACTIONr_angle_refined_deg1.541.97311138
X-RAY DIFFRACTIONr_angle_other_deg0.816318244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97351101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15223.374329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63151287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6851569
X-RAY DIFFRACTIONr_chiral_restr0.0930.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021773
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_it8.0244.2114374
X-RAY DIFFRACTIONr_mcbond_other8.014.214373
X-RAY DIFFRACTIONr_mcangle_it8.4226.5145461
X-RAY DIFFRACTIONr_mcangle_other8.4226.5165462
X-RAY DIFFRACTIONr_scbond_it16.3135.4593824
X-RAY DIFFRACTIONr_scbond_other16.3125.4593824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.6177.875670
X-RAY DIFFRACTIONr_long_range_B_refined14.72518.769422
X-RAY DIFFRACTIONr_long_range_B_other14.72418.7619423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3802 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.440.5
2BMEDIUM POSITIONAL0.390.5
3CMEDIUM POSITIONAL0.410.5
4DMEDIUM POSITIONAL0.490.5
1AMEDIUM THERMAL7.445
2BMEDIUM THERMAL6.215
3CMEDIUM THERMAL6.65
4DMEDIUM THERMAL8.065
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 169 -
Rwork0.235 5440 -
obs--91.31 %

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