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- PDB-5tjj: Crystal structure of IcIR transcriptional regulator from Alicyclo... -

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Basic information

Entry
Database: PDB / ID: 5tjj
TitleCrystal structure of IcIR transcriptional regulator from Alicyclobacillus acidocaldarius
ComponentsTranscriptional regulator, IclR family
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
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. / ArsR-like helix-turn-helix domain / GAF domain / GAF-like domain superfamily ...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. / ArsR-like helix-turn-helix domain / 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
Transcriptional regulator, IclR family
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMichalska, K. / Mack, J.C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of IcIR transcriptional regulator from Alicyclobacillus acidocaldarius
Authors: Michalska, K. / Mack, J.C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, IclR family
B: Transcriptional regulator, IclR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1373
Polymers58,0452
Non-polymers921
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-34 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.380, 98.380, 119.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transcriptional regulator, IclR family


Mass: 29022.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A) (bacteria)
Strain: ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A
Gene: Aaci_0162 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Magic / References: UniProt: C8WQP8
#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.: 44 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M succinic acid, pH 7.0, cryo 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20970 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.56
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.99 / CC1/2: 0.632 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.669 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.268 / Stereochemistry target values: Maximum likelihood / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1051 5 %RANDOM
Rwork0.18967 ---
obs0.19198 19818 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.61 Å20 Å2
3---1.22 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 6 44 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194029
X-RAY DIFFRACTIONr_bond_other_d0.0020.023907
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9645468
X-RAY DIFFRACTIONr_angle_other_deg0.96238937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18522.623183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02938
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_it1.1653.2432014
X-RAY DIFFRACTIONr_mcbond_other1.1643.2422013
X-RAY DIFFRACTIONr_mcangle_it1.9214.8612514
X-RAY DIFFRACTIONr_mcangle_other1.924.8622515
X-RAY DIFFRACTIONr_scbond_it1.6163.5452015
X-RAY DIFFRACTIONr_scbond_other1.6153.5452015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.65.2162955
X-RAY DIFFRACTIONr_long_range_B_refined3.53237.7774282
X-RAY DIFFRACTIONr_long_range_B_other3.53237.794283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 80 -
Rwork0.253 1414 -
obs--99.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.1912-1.2322.095.7576-1.51272.0934-0.00330.03590.33260.3427-0.1181-0.2165-0.31630.26310.12140.1621-0.06240.0210.0594-0.01950.056477.379559.654350.0908
23.39950.70312.43472.46090.77397.3993-0.0999-0.0497-0.08730.3562-0.0001-0.02090.16080.27730.10.07050.01350.00640.01850.01560.070574.965445.848748.1182
310.881-4.88754.9155.6341-1.99384.40630.07040.0547-0.0434-0.0082-0.0448-0.03410.05620.1172-0.02560.0603-0.05240.04660.0527-0.04270.038781.282536.983123.1881
45.1071-0.58592.46720.87420.14062.26370.28480.63310.017-0.044-0.0799-0.08830.19880.431-0.20490.14410.04650.01960.1774-0.02810.070794.526137.455818.9481
52.51220.1806-1.16382.97882.00528.30350.08760.12120.2244-0.1326-0.0740.1077-0.10550.0667-0.01370.01050.0074-0.00060.0170.01580.104985.395445.746321.8076
62.8594-1.33911.44573.3098-1.32152.6308-0.1361-0.10460.1980.09940.10660.1106-0.2317-0.09620.02960.049-0.01820.02120.0304-0.02680.053165.330548.694744.6089
74.6194-0.5268-0.3372.688-0.95796.1216-0.1262-0.03980.020.13060.07040.16550.160.01290.05590.0301-0.0265-0.00630.07320.02640.096768.421833.429660.4595
80.05640.0758-0.00529.25771.54290.2653-0.051-0.092-0.0866-0.110.00210.1133-0.02810.0360.0490.31410.02220.05020.31690.01060.270856.640541.185872.2009
95.25060.79960.13853.77450.74495.47910.043-0.83320.31950.6894-0.16250.3744-0.0756-0.27910.11940.14290.00250.08080.1499-0.03820.105864.993831.37171.049
1010.01936.25631.2947.43310.74452.96-0.03420.0572-0.3511-0.0472-0.0543-0.27760.1160.22890.08850.07620.08650.01370.14420.00910.03374.637124.184264.6681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 91
3X-RAY DIFFRACTION3A92 - 121
4X-RAY DIFFRACTION4A122 - 184
5X-RAY DIFFRACTION5A185 - 254
6X-RAY DIFFRACTION6B3 - 91
7X-RAY DIFFRACTION7B92 - 154
8X-RAY DIFFRACTION8B155 - 167
9X-RAY DIFFRACTION9B168 - 218
10X-RAY DIFFRACTION10B219 - 252

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