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- PDB-3mq0: Crystal Structure of Agobacterium tumefaciens repressor BlcR -

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Basic information

Entry
Database: PDB / ID: 3mq0
TitleCrystal Structure of Agobacterium tumefaciens repressor BlcR
ComponentsTranscriptional repressor of the blcABC operon
KeywordsTranscription repressor / helix-turn-helix / GAF fold
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/SIR / Resolution: 1.793 Å
AuthorsChen, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Agrobacterium tumefaciens Transcription Factor BlcR Is Regulated via Oligomerization.
Authors: Pan, Y. / Fiscus, V. / Meng, W. / Zheng, Z. / Zhang, L.H. / Fuqua, C. / Chen, L.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: Transcriptional repressor of the blcABC operon
B: Transcriptional repressor of the blcABC operon


Theoretical massNumber of molelcules
Total (without water)59,6302
Polymers59,6302
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.155, 74.773, 141.808
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 Transcriptional repressor of the blcABC operon


Mass: 29814.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: A6 / Gene: AGR_pAT_196, attJ, Atu5136, blcR / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8VPD8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 9% PEG400, 30 mM MgCl2, 30 mM MES, pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00826 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008
Details: osenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00826 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 51988 / Num. obs: 48827 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 25.1
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.27 / Num. unique all: 5108 / % possible all: 71.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD/SIR / Resolution: 1.793→26.518 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1892 4.1 %random
Rwork0.1871 ---
obs0.1884 46106 88.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.303 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5589 Å2-0 Å20 Å2
2---1.63 Å2-0 Å2
3---3.1889 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.793→26.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 0 378 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073788
X-RAY DIFFRACTIONf_angle_d1.0375134
X-RAY DIFFRACTIONf_dihedral_angle_d13.5621395
X-RAY DIFFRACTIONf_chiral_restr0.064605
X-RAY DIFFRACTIONf_plane_restr0.005669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7934-1.83830.2593850.22592119X-RAY DIFFRACTION60
1.8383-1.88790.25371050.21472446X-RAY DIFFRACTION70
1.8879-1.94350.25711130.2042524X-RAY DIFFRACTION73
1.9435-2.00620.22011260.20352884X-RAY DIFFRACTION82
2.0062-2.07790.24291350.20063051X-RAY DIFFRACTION87
2.0779-2.1610.22451440.18683246X-RAY DIFFRACTION92
2.161-2.25930.22911370.17553315X-RAY DIFFRACTION94
2.2593-2.37840.21211410.17643366X-RAY DIFFRACTION96
2.3784-2.52730.24531450.18543414X-RAY DIFFRACTION96
2.5273-2.72220.2231440.18833471X-RAY DIFFRACTION98
2.7222-2.99580.23041510.19373518X-RAY DIFFRACTION99
2.9958-3.42860.22471550.18733585X-RAY DIFFRACTION100
3.4286-4.31660.18071550.16223609X-RAY DIFFRACTION100
4.3166-26.5210.20391560.1893666X-RAY DIFFRACTION97
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)
10.9971-1.04850.04371.23920.21970.41710.0530.17310.3020.13220.0563-0.3011-0.07220.062-00.0968-0.0287-0.01430.1811-0.0380.1804-26.133340.529138.9088
20.41150.0627-0.08020.3711-0.29430.3711-0.00820.0887-0.38880.55060.2646-0.73470.01130.2508-0.00010.1750.0371-0.0640.2479-0.04140.2704-23.483331.885840.3728
30.5935-0.81290.78081.4981-0.23421.03490.26330.3094-0.4802-0.1096-0.04560.0760.11410.14940.00360.09480.01250.02990.1926-0.03640.0856-38.180732.426926.1271
41.985-0.0527-0.49232.60380.89721.49770.02860.0280.0155-0.3377-0.18230.3556-0.3927-0.0953-0.00070.22030.0442-0.00920.0666-0.0420.1765-55.7242.10384.5625
50.88710.6237-0.68451.8251.04182.40190.10840.00980.2799-0.5554-0.18590.2915-0.5364-0.07170.00040.32770.0617-0.03360.1082-0.01830.2549-54.446648.76697.216
60.76070.09620.12710.82690.2220.5622-0.1443-0.77050.66780.287-0.0845-0.3517-0.48510.0970.01090.29480.0239-0.00280.1137-0.09150.3137-51.176850.46218.115
71.64250.3845-0.87731.7739-0.35131.58820.01330.168-0.13580.0708-0.04180.04010.1279-0.21990.00010.0575-0.0079-0.01510.1078-0.0210.1437-41.0229.40336.1806
82.30321.23090.54921.90770.80581.08590.1221-0.16790.05730.0974-0.0788-0.0647-0.18490.16210.00990.151-0.0278-0.01540.135-0.01820.0989-8.288420.908119.9649
90.122-0.11530.17381.08980.42240.9299-0.01460.12960.0555-0.2636-0.03610.1425-0.12160.1034-0.00020.1774-0.0226-0.01270.164-0.02130.066-13.480216.58783.7963
100.5740.33850.54280.4428-0.01730.93940.18670.1284-0.3866-0.1529-0.0274-0.16050.20350.17930.00180.13530.0298-0.02070.1439-0.04740.0821-11.53666.9565.6821
110.93721.02840.32841.2164-0.08061.63590.06840.1423-0.1103-0.1088-0.1158-0.1106-0.03720.1007-0.00010.07920.0134-0.00980.1083-0.00750.0392-10.463214.089915.5977
120.84260.43680.28791.0156-0.56970.70470.0635-0.3579-0.16070.147800.22450.1049-0.02370.01050.1422-0.01910.01720.13290.00220.0842-16.53711.606123.3744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:56)
2X-RAY DIFFRACTION2(chain A and resid 57:77)
3X-RAY DIFFRACTION3(chain A and resid 78:111)
4X-RAY DIFFRACTION4(chain A and resid 112:195)
5X-RAY DIFFRACTION5(chain A and resid 196:244)
6X-RAY DIFFRACTION6(chain A and resid 245:271)
7X-RAY DIFFRACTION7(chain B and resid 23:100)
8X-RAY DIFFRACTION8(chain B and resid 101:145)
9X-RAY DIFFRACTION9(chain B and resid 146:181)
10X-RAY DIFFRACTION10(chain B and resid 182:214)
11X-RAY DIFFRACTION11(chain B and resid 215:244)
12X-RAY DIFFRACTION12(chain B and resid 245:272)

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