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- PDB-4ihs: Crystal Structure of BenM_DBD/catB site 1 DNA Complex -

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Basic information

Entry
Database: PDB / ID: 4ihs
TitleCrystal Structure of BenM_DBD/catB site 1 DNA Complex
Components
  • HTH-type transcriptional regulator BenM
  • catB site 1 DNA
  • catB site 1 DNA - complement
KeywordsTranscription/DNA / wHTH / HTH / Transcriptional regulator / catB promoter / 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
MALONATE ION / DNA / DNA (> 10) / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 ...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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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: catB site 1 DNA
F: catB site 1 DNA - complement
G: catB site 1 DNA
H: catB site 1 DNA - complement
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,67711
Polymers74,4508
Non-polymers2273
Water36020
1
A: HTH-type transcriptional regulator BenM
B: HTH-type transcriptional regulator BenM
E: catB site 1 DNA
F: catB site 1 DNA - complement
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3275
Polymers37,2254
Non-polymers1021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HTH-type transcriptional regulator BenM
D: HTH-type transcriptional regulator BenM
G: catB site 1 DNA
H: catB site 1 DNA - complement
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3506
Polymers37,2254
Non-polymers1252
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20370 Å2
ΔGint-130 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.493, 156.493, 141.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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

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Protein , 1 types, 4 molecules ABCD

#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

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain catB site 1 DNA


Mass: 7636.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA purchased from IDT
#3: DNA chain catB site 1 DNA - complement


Mass: 7713.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA purchased from IDT

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Non-polymers , 3 types, 23 molecules

#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.82 Å3/Da / Density % sol: 78.86 %
Crystal growTemperature: 288 K / Method: microbatch under oil / pH: 6
Details: Equal volumes of precipitant, protein solution and DNA. Precipitant: sodium malonate Crystal Screen C4- 2.4 M sodium malonate pH 6.0. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% ...Details: Equal volumes of precipitant, protein solution and DNA. Precipitant: sodium malonate Crystal Screen C4- 2.4 M sodium malonate pH 6.0. 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: 22-BM / Wavelength: 0.99999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.1→200 Å / Num. obs: 30569 / % possible obs: 92.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 99.4 Å2 / Rmerge(I) obs: 0.114 / Χ2: 3.317 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.2130.39923503.964172.5
3.21-3.344.10.32227143.544184.2
3.34-3.495.90.40130213.705193
3.49-3.6880.34631203.311196.1
3.68-3.919.50.25831583.495197.2
3.91-4.2110.30.21731993.84197.7
4.21-4.6310.30.14532232.846197.5
4.63-5.310.20.11632032.846197
5.3-6.68100.132272.967196.5
6.68-2008.70.05433543.595194.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M1E

3m1e


Resolution: 3.1→48.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.668 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1523 5 %RANDOM
Rwork0.1782 ---
obs0.1794 30320 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 268.45 Å2 / Biso mean: 108.1734 Å2 / Biso min: 55.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 2038 15 20 4995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0165275
X-RAY DIFFRACTIONr_bond_other_d0.0010.024131
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.667927
X-RAY DIFFRACTIONr_angle_other_deg0.8433.0019510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2823.586145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22115557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.371524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021024
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1452MEDIUM POSITIONAL0.460.5
1A1452MEDIUM THERMAL7.742
2B1453MEDIUM POSITIONAL0.50.5
2B1453MEDIUM THERMAL12.582
3E795MEDIUM POSITIONAL0.430.5
3E795MEDIUM THERMAL11.842
4F798MEDIUM POSITIONAL0.410.5
4F798MEDIUM THERMAL8.32
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.1650.294680.251481229867.406
3.165-3.2520.2561020.2151607218578.215
3.252-3.3460.2631140.2291662210384.451
3.346-3.4490.254800.2281802205291.715
3.449-3.5620.241940.2061753195994.283
3.562-3.6870.239930.1961695188494.904
3.687-3.8260.181700.1891686183795.591
3.826-3.9820.25850.1811620176296.765
3.982-4.1590.223780.1661532167396.234
4.159-4.3610.197820.1411465158897.418
4.361-4.5970.143750.1321401152996.534
4.597-4.8750.161770.1491290141796.471
4.875-5.2110.177640.1751236134596.654
5.211-5.6280.209570.191139124196.374
5.628-6.1630.283490.2221045114395.713
6.163-6.8880.206500.182929101896.169
6.888-7.9490.175380.13581690194.784
7.949-9.7220.149470.14165874694.504
9.722-13.6970.155160.16250355992.844
13.697-110.6570.29160.27624430382.508
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)
16.24330.13170.03685.1009-0.53812.8932-0.02270.0609-0.0446-0.27980.16020.3186-0.1535-0.1861-0.13750.1406-0.0065-0.0290.4420.04680.1062-13.9433-9.5411-54.4561
23.39644.5217-6.89810.7435-10.847416.4982-0.4673-0.335-0.7895-0.0247-0.5921-1.40990.37590.05161.05940.38960.01820.03120.81510.20360.6637-5.6288-21.7672-43.2598
30.65160.6713-0.78068.47442.304713.00930.1849-0.30240.19181.0544-0.27470.1025-0.8466-0.14380.08980.6835-0.1595-0.03950.92150.08610.2705-6.1152-8.5663-27.785
42.98258.66550.722640.75397.06191.9009-0.4726-0.06890.53041.43240.48611.8930.52160.0636-0.01351.1102-0.02310.19771.32880.15940.6173-14.8359-11.8318-26.5268
56.2105-1.4778-5.597721.09153.74355.366-0.1271-1.3008-0.07383.44390.21460.04920.5360.9957-0.08751.0658-0.1261-0.04971.33930.46740.4381-7.9673-18.5766-19.2051
64.79333.9022-5.09267.5459-8.436613.2058-0.1618-0.5459-0.67790.4976-0.965-1.1894-0.17210.83321.12680.373-0.0501-0.04350.70320.13320.42520.7089-14.8061-39.9771
756.86720.768538.48767.603814.063626.06152.51820.7968-5.30870.6350.7623-2.04831.48350.7226-3.28052.2735-0.29270.50432.7031-0.46211.522810.2951-8.919-57.556
83.1412-2.4496-0.10683.8490.52077.59140.0234-0.0796-0.864-0.0456-0.1168-0.09810.57140.41480.09340.18880.01640.00980.63340.29660.8616-0.5911-35.8095-42.6098
94.4767-2.5137-0.32035.9325-0.09044.3960.41610.0964-0.4614-0.5563-0.3686-0.30010.04490.3106-0.04750.1969-0.06420.03070.49090.08610.3709-6.447-28.3979-49.1183
104.06530.7697-3.62936.6596-2.88334.0726-0.07750.0328-0.7072-0.0977-0.19550.34020.2473-0.10920.2730.3404-0.1746-0.17420.77330.280.8177-25.8273-38.3134-41.3953
116.4778-1.1518-1.02146.4271-0.30022.73510.30560.6023-0.2126-0.3977-0.12720.3680.0407-0.7279-0.17840.1428-0.0707-0.08980.56220.11760.3244-21.9995-31.5318-49.7849
128.64268.491312.769119.623138.552778.86070.5522-0.07691.8004-0.95890.8623-0.0072-2.79911.8222-1.41442.4767-0.44030.00081.70160.17370.7576-9.5546-4.9207-7.4121
131.79050.28670.12813.5783-0.75247.71080.2132-0.37190.11290.18740.26630.5591-0.979-0.8548-0.47950.25430.11470.10540.67220.04650.4721-24.4101-1.5012-44.315
143.61210.25190.52872.9543-1.06725.08970.0352-0.18570.2430.02650.52410.8789-0.4783-0.5852-0.55930.26070.094-0.02650.54950.11560.4556-25.9147-2.3719-53.0607
154.209-0.27611.06220.2076-1.370212.44480.617-0.4792-0.44570.2995-0.02550.196-1.1419-0.5804-0.59151.5318-0.18630.21.1884-0.02730.5339-16.6419-3.9894-14.144
167.06940.1124-0.12981.6901-0.04450.9377-0.2971-1.1534-1.20410.32170.0305-0.03370.3669-0.0830.26660.3035-0.07230.08910.8240.45570.8348-21.9494-45.6653-30.8347
1716.2152-1.3884-3.965511.8041-5.98358.0044-0.7687-0.1526-0.856-0.8457-0.0159-0.94031.13630.60040.78460.490.1944-0.16611.130.2071.167917.9516-44.1026-38.6351
1858.438913.820531.09559.48565.998816.84270.0595-1.5538-0.53380.85830.2258-0.1955-0.1637-0.9366-0.28530.23750.1750.07931.43260.31141.201916.949-39.003-36.9206
199.4101-0.2279-1.00161.49310.1660.9557-0.3478-0.8209-0.85410.31360.01410.01060.4864-0.16590.33370.35-0.05680.06520.85690.47840.9762-20.9645-46.1753-30.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 58
2X-RAY DIFFRACTION2A59 - 89
3X-RAY DIFFRACTION3B1 - 28
4X-RAY DIFFRACTION4B29 - 43
5X-RAY DIFFRACTION5B44 - 58
6X-RAY DIFFRACTION6B59 - 87
7X-RAY DIFFRACTION7B88 - 93
8X-RAY DIFFRACTION8C1 - 43
9X-RAY DIFFRACTION9C44 - 90
10X-RAY DIFFRACTION10D1 - 43
11X-RAY DIFFRACTION11D44 - 89
12X-RAY DIFFRACTION12E1 - 5
13X-RAY DIFFRACTION13E6 - 25
14X-RAY DIFFRACTION14F1 - 15
15X-RAY DIFFRACTION15F16 - 25
16X-RAY DIFFRACTION16G1 - 19
17X-RAY DIFFRACTION17G20 - 25
18X-RAY DIFFRACTION18H1 - 6
19X-RAY DIFFRACTION19H7 - 25

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