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- PDB-2fx0: Crystal Structure of HlyIIR, a Hemolysin II transcriptional Regulator -

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Basic information

Entry
Database: PDB / ID: 2fx0
TitleCrystal Structure of HlyIIR, a Hemolysin II transcriptional Regulator
Componentshemolysin II regulatory protein
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


DNA binding / identical protein binding
Similarity search - Function
HTH-type transcriptional repressor NicS, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...HTH-type transcriptional repressor NicS, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Hemolysin II regulatory protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKovalevskiy, O.V. / Lebedev, A.A. / Solonin, A.S. / Antson, A.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Bacillus cereus HlyIIR, a Transcriptional Regulator of the Gene for Pore-forming Toxin Hemolysin II.
Authors: Kovalevskiy, O.V. / Lebedev, A.A. / Surin, A.K. / Solonin, A.S. / Antson, A.A.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemolysin II regulatory protein


Theoretical massNumber of molelcules
Total (without water)23,5751
Polymers23,5751
Non-polymers00
Water2,054114
1
A: hemolysin II regulatory protein

A: hemolysin II regulatory protein


Theoretical massNumber of molelcules
Total (without water)47,1502
Polymers47,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area17300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.208, 124.208, 79.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-269-

HOH

DetailsThe second subunit of biological dimer is generated by the operations: ROTATION MATRIX: 0.50000 -0.86603 0.00000 -0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS 0.00001 0.00000 66.38908 or 1-y, 1-x, 11/6-z

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Components

#1: Protein hemolysin II regulatory protein


Mass: 23575.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: B771 / Gene: hlyIIR / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: GenBank: 31322346, UniProt: Q7X506*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.76 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 40% saturation ammonium sulfate, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9792,0.9794,0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 10, 2005
RadiationMonochromator: Si 111 CHANNEL CUT / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.91841
ReflectionResolution: 2.4→25 Å / Num. all: 14561 / Num. obs: 14561 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5 / Num. unique all: 1431 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→24.68 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.633 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27648 695 4.8 %RANDOM
Rwork0.22085 ---
all0.22335 14590 --
obs0.22335 13895 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.916 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.7 Å20 Å2
2--1.39 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 0 114 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221508
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9562025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87924.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64415287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.018155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021121
X-RAY DIFFRACTIONr_nbd_refined0.2070.2746
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3890.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.211
X-RAY DIFFRACTIONr_mcbond_it1.2743930
X-RAY DIFFRACTIONr_mcangle_it1.89541437
X-RAY DIFFRACTIONr_scbond_it4.5698667
X-RAY DIFFRACTIONr_scangle_it6.78712588
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 58 -
Rwork0.281 995 -
obs--100 %
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)
13.76740.14640.46916.1794-2.18026.9948-0.1466-0.19630.36710.54890.0147-0.1999-0.54640.9860.13190.02870.15410.0119-0.1394-0.0175-0.082824.453776.528463.9587
25.7889-5.05350.468618.287-0.7237.6762-0.4506-0.9415-0.06391.18910.37070.6710.1427-0.13960.07990.04540.1920.1729-0.09810.121-0.130917.113671.186768.9095
35.1151-2.6923.42896.7550.02196.23080.35670.4152-0.1572-0.1867-0.08610.38910.1090.8644-0.2706-0.09190.15870.0538-0.09410.0474-0.097222.14170.567559.03
450.1055-2.0415-2.98456.77585.59874.660.4788-0.19571.1123-0.3941-0.51981.035-0.8585-0.83140.041-0.12550.3705-0.01390.54110.1120.015443.943666.798859.5596
514.94870.6586-3.62067.9947-0.65988.8537-0.1977-0.42490.11170.0830.4376-0.0092-1.00160.3899-0.2399-0.30320.1061-0.02560.1248-0.0144-0.133956.280661.277762.131
65.4853-2.9911-2.92648.37910.839514.224-0.5652-0.26791.16310.47410.20220.5686-1.2022-0.89340.363-0.25490.3659-0.02010.50860.0792-0.099246.912963.633168.3292
726.202322.746513.797124.00967.061412.93390.4781-2.39791.3372-0.0041-1.02360.71370.1410.3560.5455-0.12910.4832-0.00710.6398-0.19520.007536.483866.875972.6266
88.5237-4.3009-0.4744.42441.2210.4540.69970.8447-0.405-0.4447-0.83580.17360.15990.56870.1361-0.10080.37020.00290.39010.1892-0.11931.526357.186561.4708
99.1861-2.7630.31712.4177-1.98228.3918-0.0814-0.3192-0.5515-0.1340.25230.12020.1634-0.7874-0.1709-0.37110.0151-0.01420.21990.0817-0.018253.712351.134562.0258
104.0089-2.4065-4.92081.44462.95396.0402-0.55030.1562-0.07330.56470.3933-0.22820.4511-0.08930.157-0.24530.0652-0.00370.47970.22570.101841.594351.28674.1652
1115.5502-5.5539-2.414614.25932.738310.2844-0.3623-1.2222-0.25390.99580.596-0.0839-0.0766-0.295-0.2337-0.28240.0625-0.00620.3310.0964-0.22453.616153.587774.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 21
2X-RAY DIFFRACTION2A22 - 41
3X-RAY DIFFRACTION3A42 - 62
4X-RAY DIFFRACTION4A63 - 71
5X-RAY DIFFRACTION5A72 - 84
6X-RAY DIFFRACTION6A85 - 91
7X-RAY DIFFRACTION7A92 - 102
8X-RAY DIFFRACTION8A103 - 128
9X-RAY DIFFRACTION9A129 - 143
10X-RAY DIFFRACTION10A144 - 169
11X-RAY DIFFRACTION11A186 - 198

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