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- PDB-4iht: Crystal Structure of BenM_DBD/benA site 1 DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4iht
TitleCrystal Structure of BenM_DBD/benA site 1 DNA Complex
Components
  • HTH-type transcriptional regulator BenM
  • benA site 1 DNA
  • benA site 1 DNA - complement
KeywordsTranscription/DNA / wHTH / HTH / Transcriptional Regulator / benA promoter site 1 / Transcription-DNA complex
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 / 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
DNA / DNA (> 10) / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAlanazi, A. / Momany, C. / Neidle, E.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators.
Authors: Alanazi, A.M. / Neidle, E.L. / Momany, C.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 2007
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.
#3: 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.r
Authors: Ezezika, O.C. / Haddad, S. / Neidle, E.L. / Momany, C.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator BenM
B: HTH-type transcriptional regulator BenM
C: HTH-type transcriptional regulator BenM
D: HTH-type transcriptional regulator BenM
E: benA site 1 DNA
F: benA site 1 DNA - complement
G: benA site 1 DNA
H: benA site 1 DNA - complement


Theoretical massNumber of molelcules
Total (without water)74,4508
Polymers74,4508
Non-polymers00
Water543
1
A: HTH-type transcriptional regulator BenM
B: HTH-type transcriptional regulator BenM
E: benA site 1 DNA
F: benA site 1 DNA - complement


Theoretical massNumber of molelcules
Total (without water)37,2254
Polymers37,2254
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-58 kcal/mol
Surface area16030 Å2
MethodPISA
2
C: HTH-type transcriptional regulator BenM
D: HTH-type transcriptional regulator BenM
G: benA site 1 DNA
H: benA site 1 DNA - complement


Theoretical massNumber of molelcules
Total (without water)37,2254
Polymers37,2254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-57 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.956, 300.295, 46.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24H
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
HTH-type transcriptional regulator BenM / Ben and cat operon transcriptional regulator / TRANSCRIPTIONAL REGULATOR BENM DNA BINDING DOMAIN


Mass: 10937.559 Da / Num. of mol.: 4 / Fragment: UNP residues 1-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter sp. (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: DNA chain benA site 1 DNA


Mass: 7654.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA purchased from IDT
#3: DNA chain benA site 1 DNA - complement


Mass: 7695.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA purchased from IDT
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 288 K / Method: microbatch under oil / pH: 6.5
Details: Equal volumes of precipitant, protein solution and DNA. Precipitant: Optimized index screen 79- 25 mM bis-tris, 25% PEG 3000, 50 mM ammonium acetate. Protein: 20 mM Tris base (pH 8.0), 0.5 M ...Details: Equal volumes of precipitant, protein solution and DNA. Precipitant: Optimized index screen 79- 25 mM bis-tris, 25% PEG 3000, 50 mM ammonium acetate. 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: 0.97934 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17712 / % possible obs: 92.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 99.4 Å2 / Rmerge(I) obs: 0.065 / Χ2: 3.411 / Net I/σ(I): 21.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.953.30.5038751.842192.9
2.95-34.10.3968871.788196
3-3.064.10.3188872.035196.5
3.06-3.123.90.2749252.297196.8
3.12-3.193.90.2148542.883195
3.19-3.273.90.1539302.872195.1
3.27-3.353.80.1438473.119195.1
3.35-3.443.70.1318973.51194.3
3.44-3.543.80.1199093.796194.3
3.54-3.653.60.1118683.873194.2
3.65-3.783.70.098774.145193
3.78-3.943.50.0848994.12193.1
3.94-4.113.50.0758654.235194.1
4.11-4.333.50.0648864.421193.2
4.33-4.63.50.0598984.196191.6
4.6-4.963.50.0568794.148191.4
4.96-5.463.50.0558714.157191
5.46-6.243.60.0539034.198191
6.24-7.863.50.0438933.715188.9
7.86-503.50.0398623.671178.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M1E

3m1e


Resolution: 3→31.66 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 42.265 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 820 5.1 %RANDOM
Rwork0.1845 ---
obs0.1877 15998 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.28 Å2 / Biso mean: 95.0928 Å2 / Biso min: 49.94 Å2
Baniso -1Baniso -2Baniso -3
1-8.54 Å20 Å20 Å2
2---2.54 Å20 Å2
3----6 Å2
Refinement stepCycle: LAST / Resolution: 3→31.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 2038 0 3 4913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0165209
X-RAY DIFFRACTIONr_bond_other_d0.0010.024088
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.6587840
X-RAY DIFFRACTIONr_angle_other_deg0.8423.0019412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47523.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60115552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1141524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021003
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1417MEDIUM POSITIONAL0.320.5
1A1417MEDIUM THERMAL8.322
2B1453MEDIUM POSITIONAL0.330.5
2B1453MEDIUM THERMAL7.492
3E795MEDIUM POSITIONAL0.360.5
3E795MEDIUM THERMAL5.562
4F798MEDIUM POSITIONAL0.320.5
4F798MEDIUM THERMAL5.442
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 61 -
Rwork0.272 1039 -
all-1100 -
obs--96.32 %
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)
15.6548-2.22081.36766.31363.49757.37720.13460.2736-0.0773-0.0559-0.12050.54280.5104-0.2462-0.01410.1274-0.0134-0.10790.128-0.00970.143822.0757-53.158-8.077
25.0011-1.91640.48352.5041-1.37622.1362-0.4121-0.4847-0.01290.18910.2870.16940.6962-0.14130.12510.51040.00490.0540.2858-0.0210.31620.0832-51.1383.1155
34.3146-1.8395-2.90977.12680.98464.6060.4181-0.07790.7229-0.7317-0.1181-0.2819-0.4149-0.1062-0.30.12340.0628-0.00360.2476-0.08460.512321.4248-28.4645-2.1059
417.177820.4123-7.259327.5226-1.198320.15420.10921.21341.4981-0.39261.5981.4001-1.72830.0414-1.70720.65120.21310.15370.66290.00410.906613.0842-21.70044.0527
510.1158-7.254-0.288410.05131.20191.2507-0.2845-1.24680.21270.3730.4606-0.12870.0377-0.0189-0.17620.03390.0164-0.05460.3225-0.05340.166825.9942-42.42788.8393
68.82012.86890.98147.775-2.09018.5838-0.32410.5027-0.42330.11010.4842-0.69750.07170.5404-0.16010.04570.0834-0.0290.3543-0.14120.095457.8006-47.30985.9597
729.2203-3.215120.59688.0909-0.371815.17810.6490.31880.01020.5422-0.54730.380.69840.1052-0.10180.13290.0599-0.05830.2912-0.04130.212549.1669-48.2999.9322
86.5113-2.0734-0.84619.0758-2.92766.4641-0.2288-0.4727-0.86470.1320.91830.65211.26280.1902-0.68960.57080.1149-0.12440.5494-0.17790.531351.2661-58.76674.0548
95.46229.552-0.4128.2262-2.78144.5222-0.81051.23310.5073-1.93840.9095-0.5539-0.2760.6981-0.0990.1955-0.15780.01530.93260.07570.303656.9484-39.9588-7.4953
100.7027-0.4445-1.97339.59331.3029.6626-0.28140.23940.2766-0.13310.22210.8538-0.8043-0.39660.05940.6246-0.1648-0.43580.3540.30150.592544.5063-24.87230.2092
114.7765-0.3686-5.73066.38633.66648.77250.11070.15640.331-0.53530.1209-0.3887-0.78450.1388-0.23160.6208-0.2045-0.37340.52320.40510.766852.1342-18.41260.3128
123.80097.7951-1.15724.5688-3.42962.1446-1.11841.09260.0013-2.26541.1371-0.3201-0.20780.2952-0.01860.7422-0.3285-0.06640.78510.02030.298147.0149-38.5346-9.3561
135.4256-3.6571-1.815512.587-0.19029.5716-0.1483-0.14730.61990.2861-0.0032-0.0045-0.88970.18770.15140.84340.24730.15290.2151-0.05470.795919.0254-12.4118-7.4369
142.5039-0.7781-0.648613.22281.23852.79130.14910.3748-0.095-0.8482-0.3213-0.6808-0.1514-0.36370.17220.28140.055-0.00370.3592-0.01390.130324.978-49.4125-21.3488
153.36210.2617-0.80295.43512.05222.02790.41760.2681-0.1184-0.1933-0.5094-0.3324-0.1392-0.46880.09180.28570.0691-0.08490.3167-0.0020.13324.1297-50.3686-20.4227
1611.3702-5.3841-7.07415.33547.484611.82930.25990.18840.805-0.932-0.43340.3605-0.9713-0.52050.17350.78510.12930.04750.2050.05830.816318.2789-12.0365-10.0309
172.7536-3.21651.617415.2102-4.11692.7904-0.39690.1640.78271.5932-0.05360.1542-1.16810.03920.45050.58170.1237-0.12820.29850.01250.364647.896-23.64115.3403
182.71732.515-1.960915.94873.80684.2486-0.4689-0.3573-0.97351.27330.0584-0.37211.18440.3450.41040.61650.2948-0.07980.24050.11910.883653.0361-62.956420.4606
1918.2765-11.8512-1.536818.9925-8.900117.0571-0.1819-0.2523-0.71850.6008-0.3933-1.08491.03031.3330.57520.50280.1523-0.37110.2925-0.06410.668158.2589-62.518718.6356
201.9775-0.57940.98958.2254-3.74423.77520.05690.05780.76991.1512-0.6080.4718-1.18360.28360.55110.64380.1244-0.0440.2753-0.01890.508847.5796-24.32816.0554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 89
3X-RAY DIFFRACTION3B1 - 43
4X-RAY DIFFRACTION4B44 - 58
5X-RAY DIFFRACTION5B59 - 90
6X-RAY DIFFRACTION6C1 - 28
7X-RAY DIFFRACTION7C29 - 43
8X-RAY DIFFRACTION8C44 - 58
9X-RAY DIFFRACTION9C59 - 86
10X-RAY DIFFRACTION10D1 - 28
11X-RAY DIFFRACTION11D29 - 58
12X-RAY DIFFRACTION12D59 - 90
13X-RAY DIFFRACTION13E1 - 8
14X-RAY DIFFRACTION14E9 - 25
15X-RAY DIFFRACTION15F1 - 17
16X-RAY DIFFRACTION16F18 - 25
17X-RAY DIFFRACTION17G1 - 19
18X-RAY DIFFRACTION18G20 - 25
19X-RAY DIFFRACTION19H1 - 6
20X-RAY DIFFRACTION20H7 - 25

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