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- PDB-7dqb: Crystal structure of an IclR homolog complexed with 4-hydroxybenz... -

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Basic information

Entry
Database: PDB / ID: 7dqb
TitleCrystal structure of an IclR homolog complexed with 4-hydroxybenzoate from Microbacterium hydrocarbonoxydans in P212121 form
ComponentsIclR homolog
KeywordsTRANSCRIPTION / Complex
Function / homologyP-HYDROXYBENZOIC ACID
Function and homology information
Biological speciesMicrobacterium hydrocarbonoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsAkiyama, T. / Sasaki, Y. / Ito, S. / 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
DepositionDec 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: IclR homolog
B: IclR homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9244
Polymers58,6472
Non-polymers2762
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-30 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.071, 74.642, 104.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IclR homolog


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-PHB / P-HYDROXYBENZOIC ACID


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic, 2.0 M sodium chloride, and 1 mM 4-HBA

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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: 2.1→50 Å / Num. obs: 27794 / % possible obs: 94.6 % / Redundancy: 3.8 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1382 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H1A

5h1a


Resolution: 2.101→48.222 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.93 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2189 1405 5.062 %
Rwork0.2147 26350 -
all0.215 --
obs-27755 94.559 %
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: 35.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.496 Å20 Å2-0 Å2
2---0.716 Å2-0 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.101→48.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 20 77 3751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133726
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173744
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.6375060
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5688534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.92718.654208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0971552
X-RAY DIFFRACTIONr_chiral_restr0.0580.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
X-RAY DIFFRACTIONr_nbd_refined0.1980.2722
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23295
X-RAY DIFFRACTIONr_nbtor_refined0.1430.21798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3690.26
X-RAY DIFFRACTIONr_nbd_other0.2560.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.24
X-RAY DIFFRACTIONr_mcbond_it1.533.6341918
X-RAY DIFFRACTIONr_mcbond_other1.5243.6331917
X-RAY DIFFRACTIONr_mcangle_it2.4585.4462394
X-RAY DIFFRACTIONr_mcangle_other2.4585.4472395
X-RAY DIFFRACTIONr_scbond_it2.0143.9811808
X-RAY DIFFRACTIONr_scbond_other2.0133.981809
X-RAY DIFFRACTIONr_scangle_it3.2545.852666
X-RAY DIFFRACTIONr_scangle_other3.2535.8492667
X-RAY DIFFRACTIONr_lrange_it4.56143.3623899
X-RAY DIFFRACTIONr_lrange_other4.56143.3583897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.1550.3211040.3051920X-RAY DIFFRACTION95.3817
2.155-2.2140.294900.2781939X-RAY DIFFRACTION96.6651
2.214-2.2780.267790.2641848X-RAY DIFFRACTION96.3982
2.278-2.3480.2971000.2661810X-RAY DIFFRACTION96.3187
2.348-2.4250.26830.2421768X-RAY DIFFRACTION96.3059
2.425-2.510.276930.2421672X-RAY DIFFRACTION95.8718
2.51-2.6050.251830.2431622X-RAY DIFFRACTION95.7327
2.605-2.7110.305820.2521565X-RAY DIFFRACTION95.3125
2.711-2.8310.232930.2351481X-RAY DIFFRACTION95.1632
2.831-2.9690.242820.2321427X-RAY DIFFRACTION94.6082
2.969-3.1290.253760.2261352X-RAY DIFFRACTION94.382
3.129-3.3180.228710.2241282X-RAY DIFFRACTION94.2201
3.318-3.5470.178750.2021188X-RAY DIFFRACTION93.5556
3.547-3.830.214750.1951101X-RAY DIFFRACTION93.2593
3.83-4.1930.167490.1761052X-RAY DIFFRACTION92.4433
4.193-4.6860.165430.156926X-RAY DIFFRACTION91.6745
4.686-5.4050.185440.189822X-RAY DIFFRACTION90.9664
5.405-6.6070.221320.214699X-RAY DIFFRACTION90.1356
6.607-9.2890.117320.154552X-RAY DIFFRACTION89.1603
9.289-48.20.166190.206324X-RAY DIFFRACTION85.3234

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