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- PDB-5h1a: Crystal structure of an IclR homolog from Microbacterium sp. stra... -

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Basic information

Entry
Database: PDB / ID: 5h1a
TitleCrystal structure of an IclR homolog from Microbacterium sp. strain HM58-2
ComponentsIclR transcription factor homolog
KeywordsTRANSCRIPTION REGULATOR / DNA-binding
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesMicrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAkiyama, T. / Yamada, Y. / Takaya, N. / Ito, S. / Sasaki, Y. / Yajima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS15K07369 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.
Authors: Akiyama, T. / Yamada, Y. / Takaya, N. / Ito, S. / Sasaki, Y. / Yajima, S.
History
DepositionOct 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 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: IclR transcription factor homolog
B: IclR transcription factor homolog
C: IclR transcription factor homolog
D: IclR transcription factor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3905
Polymers117,2954
Non-polymers951
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: IclR transcription factor homolog
B: IclR transcription factor homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7423
Polymers58,6472
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area22230 Å2
MethodPISA
3
C: IclR transcription factor homolog
D: IclR transcription factor homolog


Theoretical massNumber of molelcules
Total (without water)58,6472
Polymers58,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-25 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.889, 155.375, 83.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
IclR transcription factor homolog


Mass: 29323.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8 / Details: 1M (NH4)2HPO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.038 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 69549 / % possible obs: 98.9 % / Redundancy: 6.7 % / Net I/σ(I): 24.9
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24187 3489 5 %RANDOM
Rwork0.22688 ---
obs0.22763 66018 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.174 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-
2--0.37 Å20 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.1→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 5 125 7472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197453
X-RAY DIFFRACTIONr_bond_other_d00.027540
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.97810127
X-RAY DIFFRACTIONr_angle_other_deg3.675317177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72521.672317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.474151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.78215103
X-RAY DIFFRACTIONr_chiral_restr0.0760.21217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218394
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021669
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_it1.6683.7253843
X-RAY DIFFRACTIONr_mcbond_other1.6673.7253842
X-RAY DIFFRACTIONr_mcangle_it2.7735.5764795
X-RAY DIFFRACTIONr_mcangle_other2.7735.5764796
X-RAY DIFFRACTIONr_scbond_it1.9734.1013610
X-RAY DIFFRACTIONr_scbond_other1.9694.13607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3146.025327
X-RAY DIFFRACTIONr_long_range_B_refined4.92944.2917757
X-RAY DIFFRACTIONr_long_range_B_other4.92944.2697745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 243 -
Rwork0.283 4489 -
obs--92.08 %

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