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- PDB-7cuo: IclR transcription factor complexed with 4-hydroxybenzoic acid fr... -

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Basic information

Entry
Database: PDB / ID: 7cuo
TitleIclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans
ComponentsTranscription factor
KeywordsGENE REGULATION / Complex
Function / homologyP-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAkiyama, T. / Ito, S. / Sasaki, Y. / Yajima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K05398 Japan
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding.
Authors: Akiyama, T. / Sasaki, Y. / Ito, S. / Yajima, S.
History
DepositionAug 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor
B: Transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,69212
Polymers58,6472
Non-polymers1,04510
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-139 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.080, 83.080, 203.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Transcription factor


Mass: 29323.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES monohydrate, pH 6.5, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic and 2.0 M sodium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49164 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3550 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5h1a

5h1a


Resolution: 2→44.484 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.673 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2179 2407 4.897 %
Rwork0.2019 46750 -
all0.203 --
obs-49157 99.927 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.131 Å2
Baniso -1Baniso -2Baniso -3
1-1.362 Å2-0 Å2-0 Å2
2--1.362 Å20 Å2
3----2.725 Å2
Refinement stepCycle: LAST / Resolution: 2→44.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 60 210 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133785
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173714
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.6375147
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5668506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9118.732213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47715640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141553
X-RAY DIFFRACTIONr_chiral_restr0.0630.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
X-RAY DIFFRACTIONr_nbd_refined0.2030.2732
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23294
X-RAY DIFFRACTIONr_nbtor_refined0.1470.21795
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2130.216
X-RAY DIFFRACTIONr_nbd_other0.1850.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0770.21
X-RAY DIFFRACTIONr_mcbond_it1.6782.8741928
X-RAY DIFFRACTIONr_mcbond_other1.6672.8731927
X-RAY DIFFRACTIONr_mcangle_it2.6544.2982410
X-RAY DIFFRACTIONr_mcangle_other2.6544.2992411
X-RAY DIFFRACTIONr_scbond_it2.3683.3221857
X-RAY DIFFRACTIONr_scbond_other2.3673.3231858
X-RAY DIFFRACTIONr_scangle_it3.8734.8292737
X-RAY DIFFRACTIONr_scangle_other3.8724.832738
X-RAY DIFFRACTIONr_lrange_it5.5134.7594043
X-RAY DIFFRACTIONr_lrange_other5.47134.6524013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2531590.2583386X-RAY DIFFRACTION99.8873
2.052-2.1080.2531940.2413299X-RAY DIFFRACTION99.9714
2.108-2.1690.2691600.2353212X-RAY DIFFRACTION100
2.169-2.2360.2421510.2183153X-RAY DIFFRACTION100
2.236-2.3090.2511560.1973060X-RAY DIFFRACTION99.9689
2.309-2.390.2071570.1982927X-RAY DIFFRACTION99.9676
2.39-2.480.2081360.1982851X-RAY DIFFRACTION99.9665
2.48-2.5810.2031450.1962746X-RAY DIFFRACTION99.9654
2.581-2.6960.2561320.2012636X-RAY DIFFRACTION100
2.696-2.8270.2141530.2122522X-RAY DIFFRACTION100
2.827-2.980.2141170.2092412X-RAY DIFFRACTION100
2.98-3.1610.221120.2012284X-RAY DIFFRACTION100
3.161-3.3790.203980.22175X-RAY DIFFRACTION99.9121
3.379-3.6490.2491060.22025X-RAY DIFFRACTION100
3.649-3.9960.2011040.1891872X-RAY DIFFRACTION100
3.996-4.4660.1681040.1641673X-RAY DIFFRACTION99.9438
4.466-5.1540.177730.1751545X-RAY DIFFRACTION99.9382
5.154-6.3050.24650.2231298X-RAY DIFFRACTION100
6.305-8.8870.178540.2011053X-RAY DIFFRACTION100
8.887-44.480.302310.225621X-RAY DIFFRACTION96.5926

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