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- PDB-3m1e: Crystal Structure of BenM_DBD -

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Basic information

Entry
Database: PDB / ID: 3m1e
TitleCrystal Structure of BenM_DBD
ComponentsHTH-type transcriptional regulator benM
KeywordsTranscription regulator / wHTH / Activator / Aromatic hydrocarbons catabolism / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


: / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAlanazi, A. / Momany, C. / Neidle, E.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Crystal structure of the unbound LysR-type transcriptional regulator BenM DNA binding domain
Authors: Alanazi, A. / Neidle, E.L. / Momany, C.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,9612
Polymers10,9381
Non-polymers231
Water1,74797
1
A: HTH-type transcriptional regulator benM
hetero molecules

A: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9214
Polymers21,8752
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2540 Å2
ΔGint-42 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.360, 84.146, 68.734
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
11A-189-

HOH

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Components

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


Mass: 10937.559 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. ADP1 (bacteria) / Strain: ADP1 / Gene: ACIAD1435, benM, benR / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O68014
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 288 K / Method: microbatch under oil / pH: 7.5
Details: Equal volumes of precipitant and protein solution. Precipitant:Crystal Screen 2 # 30 - 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, ...Details: Equal volumes of precipitant and protein solution. Precipitant:Crystal Screen 2 # 30 - 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: MAR / Date: Nov 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.8→42.07 Å / Num. obs: 9300

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.255 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23367 437 4.8 %RANDOM
Rwork0.18547 ---
obs0.18778 8754 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 1 97 802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.984994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.438592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8423.82434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.431156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021542
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_it0.72211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.503518
X-RAY DIFFRACTIONr_scbond_it3.09678
X-RAY DIFFRACTIONr_scangle_it3.739106
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 32 -
Rwork0.276 577 -
obs--90.22 %
Refinement TLS params.Method: refined / Origin x: 6.926 Å / Origin y: -11.829 Å / Origin z: 8.502 Å
111213212223313233
T0.0574 Å2-0.0017 Å2-0.0128 Å2-0.0622 Å2-0.0185 Å2--0.0282 Å2
L1.1267 °2-0.1633 °2-0.7001 °2-2.3231 °22.8307 °2--4.406 °2
S0.0026 Å °0.0005 Å °-0.0473 Å °0.018 Å °-0.0068 Å °-0.0137 Å °0.042 Å °0.0468 Å °0.0042 Å °

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