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- PDB-2f8d: BenM effector-Binding domain crystallized from high pH conditions -

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Basic information

Entry
Database: PDB / ID: 2f8d
TitleBenM effector-Binding domain crystallized from high pH conditions
ComponentsHTH-type transcriptional regulator benM
KeywordsGENE REGULATION / BenM / LTTR / LysR-type transcriptional regulator / tetramerization / Effector binding domain / Inducer binding domain
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
BENZOIC ACID / PHOSPHATE ION / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEzezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
Authors: Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of the effector-binding domains of BenM and BenM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1.
Authors: Clark, T. / Haddad, S. / Neidle, E. / Momany, C.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

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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)53,81712
Polymers52,8032
Non-polymers1,01410
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-5 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.060, 106.401, 184.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1169-

HOH

DetailsThe biological unit is a dimer. A dimer is in the asymmetric unit.

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Components

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


Mass: 26401.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: benM / Plasmid: pet21b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 (BL21) / References: UniProt: O68014
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 455 / 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: 4.6 Å3/Da / Density % sol: 73.1 %
Crystal growpH: 10
Details: PEG 4000, glycerol, imidazole, tris, CAPS, KBr, NaCl, benzoate, pH 10, Microbatch under oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.7→92.06 Å / Num. all: 25480 / Num. obs: 25480 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Biso Wilson estimate: 53.78698 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.1
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 5.85 / Num. measured obs: 2494 / Num. unique all: 2494 / Rsym value: 0 / Χ2: 1.355 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F6G

2f6g


Resolution: 2.7→92.06 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.356 / SU ML: 0.139 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.221 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1299 5.1 %RANDOM
Rwork0.148 ---
all0.151 24162 --
obs0.151 24162 98.15 %-
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: 32.036 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2---0.06 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 68 455 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223667
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9954970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05223.765162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15215633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8541524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022747
X-RAY DIFFRACTIONr_nbd_refined0.1890.21801
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.220
X-RAY DIFFRACTIONr_mcbond_it0.7422260
X-RAY DIFFRACTIONr_mcangle_it1.63953591
X-RAY DIFFRACTIONr_scbond_it3.17671547
X-RAY DIFFRACTIONr_scangle_it4.887101376
LS refinement shellResolution: 2.695→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 103 -
Rwork0.222 1687 -
all-1790 -
obs--94.01 %

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