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- PDB-3col: Crystal structure of putative transcription regulator from Lactob... -

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Basic information

Entry
Database: PDB / ID: 3col
TitleCrystal structure of putative transcription regulator from Lactobacillus plantarum
ComponentsPutative transcription regulator
KeywordsTRANSCRIPTION REGULATOR / Lactobacillus plantarum / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription regulator, TetR family / :
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsChang, C. / Bigelow, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative transcription regulator from Lactobacillus plantarum.
Authors: Chang, C. / Bigelow, L. / Freeman, L. / Joachimiak, A.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcription regulator
B: Putative transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9863
Polymers43,8942
Non-polymers921
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-21.7 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.213, 66.936, 93.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative transcription regulator


Mass: 21947.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Species: Lactobacillus plantarum / Strain: WCFS1 / NCIMB 8826 / Gene: lp_3090 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q88T92, UniProt: F9USK4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20 % PEG 3000, 100 mM Na citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 24288 / Num. obs: 24247 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 27.27
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.71 / Num. unique all: 2372 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.321 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24618 1234 5.1 %RANDOM
Rwork0.18536 ---
all0.18838 24182 --
obs0.18838 24182 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.38 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 6 302 3021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9473923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84624.754122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91515503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1061517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21540
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22117
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8321.51890
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39622985
X-RAY DIFFRACTIONr_scbond_it2.34931112
X-RAY DIFFRACTIONr_scangle_it3.4764.5937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 86 -
Rwork0.183 1599 -
obs--95.52 %
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)
15.5881-2.02770.31194.2656-0.64047.227-0.15790.0273-0.22520.10940.0834-0.03250.27060.31170.0745-0.09630.00960.0185-0.1676-0.0181-0.155146.451746.896823.5463
23.5546-0.7943-1.38830.6528-0.03530.9701-0.10720.4117-0.0638-0.09650.10970.06360.2326-0.207-0.0025-0.0514-0.0558-0.0166-0.05080.005-0.081424.553655.594234.6643
32.7418-1.20090.19722.9914-1.76241.8843-0.0348-0.0673-0.017-0.07860.07640.0630.0980.034-0.0416-0.0231-0.00560.0011-0.0305-0.0065-0.01827.726959.673947.0208
417.60975.23694.342812.5334-1.9264.350.4259-0.0603-0.67540.0278-0.2957-1.35370.14570.6252-0.1302-0.12860.04470.0173-0.0464-0.16160.271260.085766.440436.7953
52.73150.8448-1.91920.84240.16742.8750.0939-0.36990.06890.30470.0319-0.1340.04710.2682-0.1258-0.0896-0.0059-0.0564-0.0589-0.0327-0.085441.34173.483152.2784
61.8514-0.31310.20012.7081-1.83033.7750.0020.0340.14810.13380.0174-0.0611-0.1295-0.0094-0.0194-0.0683-0.01390.0265-0.0546-0.0203-0.011630.138271.666445.4424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 5510 - 58
2X-RAY DIFFRACTION2AA56 - 14359 - 146
3X-RAY DIFFRACTION3AA144 - 193147 - 196
4X-RAY DIFFRACTION4BB8 - 5511 - 58
5X-RAY DIFFRACTION5BB56 - 14359 - 146
6X-RAY DIFFRACTION6BB144 - 193147 - 196

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