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- PDB-3k1p: Crystal Structure of full-length BenM E226K mutant -

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Basic information

Entry
Database: PDB / ID: 3k1p
TitleCrystal Structure of full-length BenM E226K mutant
ComponentsHTH-type transcriptional regulator benM
KeywordsTRANSCRIPTION / HTH / LysR-type transcriptional regulator / Activator / Aromatic hydrocarbons catabolism / DNA-binding / Transcription regulation
Function / homology
Function and homology information


catabolic process / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRuangprasert, A. / Momany, C. / Neidle, E.L. / Craven, S.H.
CitationJournal: To be Published
Title: Structure of Full-length BenM
Authors: Ruangprasert, A. / Craven, S.H. / Neidle, E.L. / Momany, C.
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)71,2902
Polymers71,2902
Non-polymers00
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-24 kcal/mol
Surface area32810 Å2
MethodPISA
2
A: HTH-type transcriptional regulator benM
B: HTH-type transcriptional regulator benM

A: HTH-type transcriptional regulator benM
B: HTH-type transcriptional regulator benM


Theoretical massNumber of molelcules
Total (without water)142,5804
Polymers142,5804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9500 Å2
ΔGint-66 kcal/mol
Surface area61100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.600, 70.700, 187.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

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


Mass: 35645.098 Da / Num. of mol.: 2 / Mutation: E226K
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) / References: UniProt: O68014
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Precipitant:20% v/v Jeffamine M-600, 0.1 M HEPES pH 7.5. Protein: 30 mM Tris base (pH 9.0), 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM BME Reservior contains 60% protein buffer, 40% ...Details: Precipitant:20% v/v Jeffamine M-600, 0.1 M HEPES pH 7.5. Protein: 30 mM Tris base (pH 9.0), 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM BME Reservior contains 60% protein buffer, 40% Crystal Screen II31, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.598
11K, H, -L20.402
ReflectionResolution: 3→50 Å / Num. all: 17861 / Num. obs: 17861 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 38.097 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Χ2: 3.168 / Net I/σ(I): 18.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1349 / Rsym value: 0.296 / Χ2: 1.721 / % possible all: 70.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F97

2f97


Resolution: 3→48.27 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.744 / SU B: 32.743 / SU ML: 0.283 / SU Rfree: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : RESIDUAL ONLY Twin refinement performed with two domains, twin fraction 0.598
RfactorNum. reflection% reflectionSelection details
Rfree0.226 922 5.2 %RANDOM
Rwork0.197 ---
all0.199 17744 --
obs0.199 17744 90.67 %-
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 max: 144.47 Å2 / Biso mean: 38.097 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--11.79 Å20 Å2
3----10.99 Å2
Refinement stepCycle: LAST / Resolution: 3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 0 373 5211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224966
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9836732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6365612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03323.722223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5815902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7421537
X-RAY DIFFRACTIONr_chiral_restr0.0710.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213715
X-RAY DIFFRACTIONr_mcbond_it1.343047
X-RAY DIFFRACTIONr_mcangle_it2.2864959
X-RAY DIFFRACTIONr_scbond_it1.98261919
X-RAY DIFFRACTIONr_scangle_it3.19381770
LS refinement shellResolution: 3→3.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 44 -
Rwork0.265 963 -
all-1007 -
obs--69.4 %
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)
18.38742.1905-0.0046.8962-4.48883.2192-0.1823-0.5967-0.37290.62260.1668-0.1548-0.4567-0.03620.01560.08740.1356-0.02081.2409-0.05170.07330.5148.174-10.514
22.941-3.1868-0.40348.2113-2.20331.5637-0.1613-0.2446-0.62620.01920.07740.980.03860.06110.08380.6462-0.0814-0.06461.2333-0.01250.947336.34756.995-17.217
37.04064.3801-3.58512.8983-2.14092.54410.2942-0.41260.54130.163-0.16030.5389-0.13181.0252-0.13390.31390.00380.00351.09140.08380.290315.8244.358-20.068
42.80271.4264-0.43525.43591.42120.64440.04240.2424-0.0277-0.48580.0428-0.2074-0.1681-0.0452-0.08520.26830.0273-0.03230.3401-0.02590.2002-12.67716.358-1.57
52.16990.58450.23581.9829-0.17721.27580.05370.02730.0188-0.0662-0.0844-0.0656-0.1080.15510.03080.26340.01820.00380.328-0.02730.2251-10.43619.3063.163
61.5729-0.20520.06552.72591.10342.53210.0571-0.02540.04210.2006-0.05820.14240.1719-0.01790.00110.3277-0.0118-0.00640.3303-0.02520.2325-20.034-4.21417.334
71.7214-0.8766-3.2194.61181.21356.21340.032-0.11590.1531-0.36910.0431-0.40770.11620.2954-0.07510.2778-0.00220.08070.45360.01920.395-10.7074.719.852
80.056-0.2472-0.13822.94230.53691.86310.0271-0.0744-0.01090.1655-0.0273-0.20750.26430.08820.00010.2609-0.0355-0.00030.3013-0.01980.2489-18.042-2.63912.253
91.99220.68910.41652.742-1.28661.9814-0.02190.00790.31860.00540.02180.0152-0.3024-0.039700.31030.0171-0.00770.338-0.03210.2537-15.25526.1964.65
104.4481-1.44383.80051.3043-1.44533.32430.2002-0.4051-0.13930.0391-0.0158-0.03720.0806-0.3174-0.18440.2871-0.10420.2430.727-0.05720.3498-26.34322.7988.351
111.861-3.32391.84846.0062-3.2772.00280.203-0.2310.1601-0.39880.1088-0.40620.1322-0.2638-0.31180.41310.07350.12321.58860.27541.413820.4925.726-15.95
120.42950.30850.49740.33010.43260.7297-0.1830.183-0.3755-0.2090.3414-0.2075-0.50.2649-0.15840.93280.3001-0.10820.83810.02951.024411.03624.466-22.021
132.7675-1.06022.22227.144-0.70531.78780.4869-0.2137-0.21451.2593-0.2995-0.39650.4137-0.1709-0.18750.8026-0.0193-0.01120.70370.13270.337827.57447.851-30.525
141.59930.6006-0.33031.4780.49821.34410.0065-0.10870.21390.0156-0.0508-0.0156-0.18370.09010.04440.2032-0.0023-0.0050.3569-0.00610.259418.42160.474-47.847
154.38530.30070.85920.20830.17660.55480.07450.2626-0.558-0.07280.0247-0.14060.05650.0408-0.09910.2286-0.01420.01830.3144-0.03040.20443.67148.869-61.214
163.2701-0.0127-0.49840.7542-1.07883.2388-0.0399-0.05980.1515-0.166-0.03590.1735-0.1248-0.10080.07590.25090.0090.01110.30710.00440.2825-0.08655.345-65.779
171.1280.36270.25521.21530.57072.8968-0.02590.19990.4571-0.2112-0.0836-0.0186-0.3909-0.05780.10950.2339-0.00860.01130.40610.04490.3776-6.70458.218-58.177
181.52180.18550.86020.16120.32031.0684-0.01070.131-0.0714-0.03560.0272-0.00350.15870.0033-0.01650.24330.01650.02370.26840.00630.23265.27450.287-58.293
195.68041.93751.0862.8855-0.4471.9874-0.0489-0.0167-0.3403-0.32430.0089-0.42410.05930.32050.03990.28570.03180.00190.3416-0.010.283528.0954.065-50.072
205.16321.5504-2.3871.6931-2.8177.70380.3323-0.02370.23420.131-0.2433-0.1493-0.36430.6624-0.0890.4754-0.0232-0.00840.27180.030.611222.72644.445-55.394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 59
3X-RAY DIFFRACTION3A60 - 88
4X-RAY DIFFRACTION4A89 - 106
5X-RAY DIFFRACTION5A107 - 163
6X-RAY DIFFRACTION6A164 - 200
7X-RAY DIFFRACTION7A201 - 215
8X-RAY DIFFRACTION8A216 - 267
9X-RAY DIFFRACTION9A268 - 294
10X-RAY DIFFRACTION10A295 - 303
11X-RAY DIFFRACTION11B1 - 48
12X-RAY DIFFRACTION12B49 - 69
13X-RAY DIFFRACTION13B70 - 92
14X-RAY DIFFRACTION14B93 - 155
15X-RAY DIFFRACTION15B156 - 175
16X-RAY DIFFRACTION16B176 - 216
17X-RAY DIFFRACTION17B217 - 240
18X-RAY DIFFRACTION18B241 - 274
19X-RAY DIFFRACTION19B275 - 294
20X-RAY DIFFRACTION20B295 - 303

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