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- PDB-5kbe: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 5kbe
TitleCRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH PHENOL
ComponentsMopR
KeywordsTRANSCRIPTION / AROMATIC SENSOR
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
: / Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 ...: / Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / NO signalling/Golgi transport ligand-binding domain superfamily / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHENOL / Phenol regulator MopR
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRay, S. / Anand, R. / Panjikar, S.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator.
Authors: Ray, S. / Gunzburg, M.J. / Wilce, M. / Panjikar, S. / Anand, R.
History
DepositionJun 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MopR
B: MopR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0936
Polymers52,7742
Non-polymers3194
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-18 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.178, 93.064, 119.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9247, -0.3765, 0.05664), (-0.3807, 0.9135, -0.1433), (0.00221, -0.1541, -0.9881)
Vector: 53.1, 10.66, 8.573)

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Components

#1: Protein MopR


Mass: 26387.182 Da / Num. of mol.: 2 / Fragment: SENSOR DOMAIN, RESIDUES 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: mopR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q43965
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M LISO4, 12% W/V PEG 6000, 0.1M TRI-SODIUM CITRATE (PH 5.6)
PH range: 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2014 / Details: MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 18123 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.13 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.63
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 7.21 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.66 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.141 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.271 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24432 923 5.1 %RANDOM
Rwork0.18209 ---
obs0.18519 17168 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 16 31 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9354460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84324.379169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01515550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1151518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022553
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.366 60 -
Rwork0.299 1094 -
obs--99.4 %

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