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- PDB-3ljl: The crystal structure of the full-length transcriptional regulato... -

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Basic information

Entry
Database: PDB / ID: 3ljl
TitleThe crystal structure of the full-length transcriptional regulator LuxT from Vibrio parahaemolyticus RIMD 2210633.
Componentstranscriptional regulator LuxT
Keywordstranscription regulator / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding
Function / homology
Function and homology information


Tetracycline repressor LuxT C-terminal domain / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsTan, K. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the full-length transcriptional regulator LuxT from Vibrio parahaemolyticus RIMD 2210633.
Authors: Tan, K. / Gu, M. / Joachimiak, A.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 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_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_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

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Assembly

Deposited unit
A: transcriptional regulator LuxT
B: transcriptional regulator LuxT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5524
Polymers36,1612
Non-polymers3902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-7 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.792, 89.792, 125.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein transcriptional regulator LuxT


Mass: 18080.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0420 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87J33
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97944
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979441
ReflectionResolution: 3.2→45 Å / Num. all: 10042 / Num. obs: 10042 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 24.5
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.67 / Num. unique all: 981 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→44.9 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.935 / SU B: 43.657 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26112 483 4.8 %RANDOM
Rwork0.22306 ---
all0.22498 9531 --
obs0.22498 9531 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.216 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å20 Å2
2--1.24 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 24 0 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9583281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43424.144111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.53515449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0351512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021793
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5421.51472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05622357
X-RAY DIFFRACTIONr_scbond_it1.7483969
X-RAY DIFFRACTIONr_scangle_it3.044.5924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.198→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 34 -
Rwork0.349 686 -
obs-720 99.45 %
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)
115.6924-3.28178.23395.6517-5.85511.71220.1845-0.8979-0.39080.10230.17870.80980.2791-0.7914-0.36320.2549-0.0655-0.03750.3820.09360.8635-10.75559.09944.25
25.7009-0.22244.23942.0361-0.800513.6814-0.193-0.22430.3866-0.04530.19520.272-0.2195-0.0459-0.00210.1771-0.0070.0115-0.0055-0.01430.81859.79854.96357.128
36.61612.64.11044.0422-1.150113.48540.20751.0534-0.5194-0.5143-0.15870.23110.12910.605-0.04880.63160.1878-0.11090.7499-0.02811.027915.93149.84822.284
412.4336-2.63550.91652.5392-1.23635.47740.3690.53470.4022-0.7525-0.202-0.3498-0.4733-0.0208-0.1670.48670.04860.07420.16140.02280.781825.74852.10644.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 62
2X-RAY DIFFRACTION2A63 - 153
3X-RAY DIFFRACTION3B5 - 62
4X-RAY DIFFRACTION4B63 - 153

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