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- PDB-2f97: Effector Binding Domain of BenM (crystals generated from high pH ... -

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Basic information

Entry
Database: PDB / ID: 2f97
TitleEffector Binding Domain of BenM (crystals generated from high pH conditions)
ComponentsHTH-type transcriptional regulator benM
KeywordsGENE REGULATION / BenM / LysR-type regulator / tetramerization / effector binding domain / inducer binding domain
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 / 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 / DI(HYDROXYETHYL)ETHER / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 CatM, LysR-type transcriptional regulators from Acinetobacter sp. ADP1.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 / 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)27,0616
Polymers26,4011
Non-polymers6605
Water4,540252
1
A: HTH-type transcriptional regulator benM
hetero molecules

A: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,12212
Polymers52,8032
Non-polymers1,31910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)70.048, 70.048, 187.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-1040-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by applying the crystallographic symmetry operation -x, y,-z.

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Strain: ADP1 / Gene: benM, benR / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: O68014
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growpH: 9
Details: PEG 8000, TAPS, LiCl, imidazole, tris, NaCl, cis,cis-muconate, glycerol, pH 9, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.2→70.014 Å / Num. all: 24724 / Num. obs: 24724 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.9 % / Biso Wilson estimate: 43.75363 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 65.96
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 5.92 / Num. measured obs: 2381 / Num. unique all: 2381 / Χ2: 1.258 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F6G

2f6g


Resolution: 2.2→70.014 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.171 / SU B: 6.52 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.14 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 1218 4.969 %RANDOM
Rwork0.1763 ---
all0.1779 23294 --
obs0.1779 23294 99.582 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 42.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.223 Å20 Å20 Å2
2--0.223 Å20 Å2
3----0.447 Å2
Refinement stepCycle: LAST / Resolution: 2.2→70.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 44 252 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221846
X-RAY DIFFRACTIONr_bond_other_d0.0010.0223
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.9962495
X-RAY DIFFRACTIONr_angle_other_deg0.309350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8125225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26723.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5251512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021373
X-RAY DIFFRACTIONr_nbd_refined0.1620.2851
X-RAY DIFFRACTIONr_nbd_other0.0970.224
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21265
X-RAY DIFFRACTIONr_nbtor_other0.0750.24
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.254
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.21
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.233
X-RAY DIFFRACTIONr_mcbond_it0.51521155
X-RAY DIFFRACTIONr_mcangle_it1.07251813
X-RAY DIFFRACTIONr_mcangle_other0.02353
X-RAY DIFFRACTIONr_scbond_it2.0997779
X-RAY DIFFRACTIONr_scbond_other0.099723
X-RAY DIFFRACTIONr_scangle_it3.24210682
X-RAY DIFFRACTIONr_scangle_other0.4161047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.2-2.2580.306860.24216250.245178196.07
2.258-2.3190.256900.20516090.207170099.941
2.319-2.3870.225950.19516060.1971701100
2.387-2.460.229930.215350.202163099.877
2.46-2.540.227780.19215170.194159699.937
2.54-2.630.179800.1914680.189155099.871
2.63-2.7290.244770.19314050.196148399.933
2.729-2.840.226720.18613810.188145499.931
2.84-2.9660.231590.1913250.192138599.928
2.966-3.110.236670.1812520.1821319100
3.11-3.2780.251620.17112110.175127499.922
3.278-3.4770.182550.15911510.16120799.917
3.477-3.7160.188540.15410870.155114299.912
3.716-4.0130.232450.15110260.154107499.721
4.013-4.3940.152500.1419350.141985100
4.394-4.9110.126390.1528650.15190599.89
4.911-5.6660.22360.1657670.167803100
5.666-6.9280.273420.216620.214704100
6.928-9.750.193240.1765410.17656799.647
9.75-70.0140.205140.2783260.27535595.775
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.7714-3.00053.77334.8933-3.45456.18010.04140.98660.0051-0.24010.01110.31170.0516-0.3357-0.0524-0.17840.0136-0.01720.11530.0201-0.032314.84726.624-4.153
23.2913-0.77570.22962.6535-0.06813.7175-0.11240.3522-0.224-0.09040.02140.04130.2962-0.18270.0911-0.1227-0.04460.02450.02170.0012-0.030919.515.676-1.48
32.4072-1.0521-0.00354.0503-0.45393.3054-0.13430.31080.1645-0.06290.11220.0415-0.2612-0.29660.022-0.18190.0098-0.01920.05210.046-0.041815.98527.8040.054
45.693-0.78186.67162.49710.28838.4255-0.4786-0.0876-0.10420.80690.39190.2971-0.6824-0.22220.08670.00110.1372-0.00650.1616-0.0092-0.027913.00331.25314.044
56.4853-2.1320.62861.319-0.03261.4216-0.2559-0.2744-0.36680.18440.13840.05830.349-0.00570.11750.00570.04280.0311-0.01620.0616-0.037933.3211.19815.508
62.613-0.06880.67233.3739-1.73645.3761-0.1497-0.1970.10570.46340.1105-0.1459-0.10660.32040.0392-0.08510.0707-0.00150.00950.0097-0.061538.82619.50518.727
78.4812-10.28712.982114.9217-0.02696.3217-0.13530.32850.45850.2174-0.0277-0.2271-0.4168-0.03620.1631-0.06030.0606-0.0160.01170.04820.024929.14629.49911.24
80.0706-0.59950.17556.0767-4.717611.007-0.1246-0.15550.17770.4320.25040.1815-0.1801-0.1606-0.1257-0.0070.09040.01030.01670.0008-0.042930.99123.35622.067
91.93280.0527-0.66123.5037-0.81334.4695-0.0655-0.06610.29370.18330.092-0.0372-0.16770.2414-0.0265-0.11910.0302-0.019-0.00580.0049-0.023741.01623.41110.807
102.0484-0.1877-0.36361.23690.16432.8247-0.1558-0.1064-0.19370.0670.0460.02360.33040.02360.1099-0.0470.03410.0128-0.03670.0422-0.041635.22712.89112.307
1115.4661-6.92147.72777.5059-3.02135.7545-0.4495-0.26990.57570.4620.04380.0086-0.1922-0.76960.4056-0.14490.02580.02870.0899-0.0042-0.055610.37426.248.439
1212.592-5.42354.099310.4245-2.00833.8881-0.10570.2119-0.2173-0.07160.11650.64450.1532-0.6534-0.0107-0.1991-0.0607-0.00650.2572-0.0120.02245.00820.9930.9
136.3539-4.077-2.549710.946-5.09610.6229-0.25970.3418-0.91280.39620.20680.93320.5301-1.03210.0529-0.1123-0.11850.03930.0981-0.00180.077211.05311.1054.028
147.9356-3.5073-6.543126.66160.64139.0383-0.43540.0726-1.20850.6133-0.10791.01190.881-0.63990.5434-0.0801-0.11760.03860.01830.01080.059912.4778.568.77
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1189 - 989 - 18
2299 - 11319 - 33
33114 - 14734 - 67
44148 - 15568 - 75
55156 - 18076 - 100
66181 - 198101 - 118
77199 - 203119 - 123
88204 - 216124 - 136
99217 - 236137 - 156
1010237 - 268157 - 188
1111269 - 277189 - 197
1212278 - 286198 - 206
1313287 - 294207 - 214
1414295 - 304215 - 224

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