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- PDB-4wxe: CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (L... -

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Basic information

Entry
Database: PDB / ID: 4wxe
TitleCRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION / LACI REGULATOR / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 ...LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS
Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)33,5826
Polymers33,3031
Non-polymers2795
Water7,422412
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-23 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.047, 108.047, 121.477
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-671-

HOH

Detailsbiological unit is a dimer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcriptional regulator, LacI family


Mass: 33302.539 Da / Num. of mol.: 1 / Fragment: UNP residues 54-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: LSEI_2103 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q036L9

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Non-polymers , 5 types, 417 molecules

#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-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (30.7 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir ((MCSG4 F4), 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 16%(w/v) PEG 4000, 0.2M Lithium Chloride, 20 %(w/v) PEG 3350); ...Details: Protein (30.7 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir ((MCSG4 F4), 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 16%(w/v) PEG 4000, 0.2M Lithium Chloride, 20 %(w/v) PEG 3350); Cryoprotection (80% Reservoir + 20% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 12, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→25.473 Å / Num. obs: 43692 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 12.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.027 / Net I/σ(I): 21.5 / Num. measured all: 964401 / Scaling rejects: 79
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 4.2 / Num. measured all: 46843 / Num. unique all: 2142 / CC1/2: 0.91 / Rpim(I) all: 0.207 / Rejects: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→25.473 Å / FOM work R set: 0.9109 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 2196 5.03 %
Rwork0.1459 41479 -
obs0.147 43675 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.47 Å2 / Biso mean: 17.81 Å2 / Biso min: 5.43 Å2
Refinement stepCycle: final / Resolution: 1.5→25.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 21 412 2551
Biso mean--17.75 30.03 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012230
X-RAY DIFFRACTIONf_angle_d1.2623044
X-RAY DIFFRACTIONf_chiral_restr0.071348
X-RAY DIFFRACTIONf_plane_restr0.007403
X-RAY DIFFRACTIONf_dihedral_angle_d13.497809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53260.19831420.181125682710
1.5326-1.56830.2041220.167125782700
1.5683-1.60750.17951300.158125682698
1.6075-1.65090.1751280.150525942722
1.6509-1.69950.18771290.145225802709
1.6995-1.75430.17031530.140625352688
1.7543-1.8170.17851380.141125842722
1.817-1.88980.16861250.143725902715
1.8898-1.97570.1631500.141725782728
1.9757-2.07990.17261190.132426032722
2.0799-2.21010.15811330.134125712704
2.2101-2.38060.16681560.135725922748
2.3806-2.620.15381470.134325832730
2.62-2.99860.19061430.144826202763
2.9986-3.77590.15181380.14426322770
3.7759-25.47690.16571430.159227032846
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19450.1195-0.11780.02680.01280.09610.00510.00090.1464-0.0316-0.01530.0267-0.05840.04510.01240.0861-0.0027-0.01510.0873-0.00130.119831.508642.509160.4562
20.1281-0.04170.11270.2166-0.00710.2382-0.00860.04690.0427-0.09280.0354-0.23350.02260.09060.01150.07820.00390.00810.08250.00410.110937.074725.872754.6739
30.17990.06890.06330.57-0.0070.29640.02690.02470.0174-0.1138-0.01780.06440.0646-0.0139-0.00610.10280.0033-0.02870.05910.00230.059522.556213.37650.7464
40.0980.0125-0.08220.10570.0390.1076-0.0013-0.12380.05790.12160.03170.0550.08990.10140.00680.0539-0.008-0.02430.0831-0.0290.062934.909428.659969.1453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 112 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 194 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 295 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 333 )A0

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