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- PDB-2h9b: Crystal structure of the effector binding domain of a BenM varian... -

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Basic information

Entry
Database: PDB / ID: 2h9b
TitleCrystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)
ComponentsHTH-type transcriptional regulator benM
KeywordsTRANSCRIPTION / LTTR / BenM / Transcriptional activator / lysR-type transcriptional regulator
Function / homology
Function and homology information


catabolic process / protein-DNA complex / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEzezika, O.C. / Craven, S.H. / Neidle, E.L. / Momany, C.
Citation
Journal: Mol.Microbiol. / Year: 2009
Title: Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.
Authors: Craven, S.H. / Ezezika, O.C. / Haddad, S. / Hall, R.A. / Momany, C. / Neidle, E.L.
#1: Journal: To be Published
Title: Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation By BenM, a LysR-type Regulator
Authors: Ezezika, O.C. / Haddad, S. / Clark, T.J. / Neidle, E.L. / Momany, C.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator benM
B: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,00312
Polymers71,2242
Non-polymers77910
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-150 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.510, 66.587, 117.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer

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Components

#1: Protein HTH-type transcriptional regulator benM / Ben and cat operon transcriptional regulator


Mass: 35611.961 Da / Num. of mol.: 2 / Fragment: Effector binding domain / Mutation: R156H, T157S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Gene: benM, benR / Plasmid: pET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O68014
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 49.9 %
Crystal growTemperature: 296.4 K
Details: Precipitant:2.0 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, Microbatch under oil, temperature 296.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48633 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.078 / Χ2: 0.858
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.464 / Num. unique obs: 4763 / Χ2: 0.799 / % possible all: 99.77

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 2F97, BenM-EBD (high pH)

2f97


Resolution: 1.8→46.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.306 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2453 5.1 %RANDOM
Rwork0.168 ---
all0.171 48557 --
obs0.171 46104 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.201 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 38 741 4227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223632
X-RAY DIFFRACTIONr_bond_other_d0.0010.023353
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9884946
X-RAY DIFFRACTIONr_angle_other_deg0.72937814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25323.727161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50915633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7561524
X-RAY DIFFRACTIONr_chiral_restr0.0590.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.1860.2734
X-RAY DIFFRACTIONr_nbd_other0.160.23664
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21762
X-RAY DIFFRACTIONr_nbtor_other0.0780.22035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2631
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.253
X-RAY DIFFRACTIONr_mcbond_it0.82322870
X-RAY DIFFRACTIONr_mcbond_other0.0712882
X-RAY DIFFRACTIONr_mcangle_it1.18753596
X-RAY DIFFRACTIONr_scbond_it2.44171629
X-RAY DIFFRACTIONr_scangle_it3.219101348
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 175 -
Rwork0.214 3305 -
obs-3480 99.77 %

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