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- PDB-2h99: Crystal structure of the effector binding domain of a BenM varian... -

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Basic information

Entry
Database: PDB / ID: 2h99
TitleCrystal structure of the effector binding domain of a BenM variant (R156H,T157S)
ComponentsHTH-type transcriptional regulator benM
KeywordsTRANSCRIPTION / LTTR / BenM / transcriptional regulation / CatM
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
ACETATE ION / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)72,12714
Polymers71,2242
Non-polymers90312
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-100 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.937, 66.506, 117.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 590 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.4 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 288.2 K / Method: microbatch under oil
Details: Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. ...Details: Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 288.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 44035 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Χ2: 0.925 / Net I/σ(I): 9.1
Reflection shellResolution: 1.85→1.92 Å / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.484 / Num. unique obs: 4281 / Χ2: 0.754 / % possible all: 99.3

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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: 1.85→44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.781 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2216 5 %RANDOM
Rwork0.165 ---
all0.167 43982 --
obs0.167 41766 99.62 %-
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: 19.128 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---0.49 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 52 578 4069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223614
X-RAY DIFFRACTIONr_bond_other_d0.0010.023366
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9914907
X-RAY DIFFRACTIONr_angle_other_deg0.73137831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31823.544158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15915631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7131525
X-RAY DIFFRACTIONr_chiral_restr0.0590.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
X-RAY DIFFRACTIONr_nbd_refined0.1940.2759
X-RAY DIFFRACTIONr_nbd_other0.1690.23672
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21749
X-RAY DIFFRACTIONr_nbtor_other0.0790.22079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2483
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.234
X-RAY DIFFRACTIONr_mcbond_it0.91722862
X-RAY DIFFRACTIONr_mcbond_other0.0872876
X-RAY DIFFRACTIONr_mcangle_it1.30653573
X-RAY DIFFRACTIONr_scbond_it2.65471611
X-RAY DIFFRACTIONr_scangle_it3.512101332
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 150 -
Rwork0.205 2974 -
obs-3124 97.53 %

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