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- PDB-3k1n: Crystal Structure of full-length BenM -

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Basic information

Entry
Database: PDB / ID: 3k1n
TitleCrystal Structure of full-length BenM
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


: / 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 / 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
IMIDAZOLE / HTH-type transcriptional regulator BenM
Similarity search - Component
Biological speciesAcinetobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 1.3Sep 6, 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
B: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4996
Polymers71,2902
Non-polymers2094
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HTH-type transcriptional regulator benM
hetero molecules

A: HTH-type transcriptional regulator benM
hetero molecules

B: HTH-type transcriptional regulator benM
hetero molecules

B: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,99812
Polymers142,5804
Non-polymers4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
crystal symmetry operation2_645-x+1,-y-1,z+1/21
crystal symmetry operation4_645x+1,-y-1,-z1
Buried area9260 Å2
ΔGint-95 kcal/mol
Surface area58660 Å2
MethodPISA
3
A: HTH-type transcriptional regulator benM
hetero molecules

A: HTH-type transcriptional regulator benM
hetero molecules

B: HTH-type transcriptional regulator benM
hetero molecules

B: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,99812
Polymers142,5804
Non-polymers4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation2_645-x+1,-y-1,z+1/21
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area11050 Å2
ΔGint-105 kcal/mol
Surface area56860 Å2
MethodPISA
4
A: HTH-type transcriptional regulator benM
hetero molecules

B: HTH-type transcriptional regulator benM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4996
Polymers71,2902
Non-polymers2094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z+1/21
Buried area3300 Å2
ΔGint-43 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.240, 70.100, 187.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-608-

HOH

21B-619-

HOH

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Components

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


Mass: 35645.031 Da / Num. of mol.: 2
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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 295 K / Method: microbatch under oil / pH: 9
Details: Precipitant: 35% v/v iso-propanol, 0.1 M Tris HCl pH 8.5, 0.2 M Ammonium acetate. Protein: 30 mM Tris base pH 9.0, 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.575
11K, H, -L20.425
ReflectionResolution: 2.99→50 Å / Num. obs: 17220 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 32.715 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 2.213 / Net I/σ(I): 15.4
Reflection shellResolution: 2.99→3.11 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.09 / Num. unique all: 1732 / Rsym value: 0.304 / Χ2: 1.505 / % possible all: 90

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F97

2f97


Resolution: 2.99→39.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.358 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : RESIDUAL ONLY Twin refinement performed with two domains, twin fraction 0.575
RfactorNum. reflection% reflectionSelection details
Rfree0.18 875 5.2 %RANDOM
Rwork0.155 ---
all0.156 16796 --
obs0.156 16796 86.85 %-
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 max: 102.14 Å2 / Biso mean: 32.715 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-7.89 Å20 Å20 Å2
2--16.23 Å20 Å2
3----24.12 Å2
Refinement stepCycle: LAST / Resolution: 2.99→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 12 263 5135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224972
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9846734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75423.767223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32515895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3511536
X-RAY DIFFRACTIONr_chiral_restr0.0930.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213718
X-RAY DIFFRACTIONr_mcbond_it2.51763042
X-RAY DIFFRACTIONr_mcangle_it3.8784946
X-RAY DIFFRACTIONr_scbond_it0.94331930
X-RAY DIFFRACTIONr_scangle_it1.5254.51788
LS refinement shellResolution: 2.99→3.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 65 -
Rwork0.2 1065 -
all-1130 -
obs--82.78 %
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)
17.5598-4.7147-1.54583.27261.15429.75210.0248-0.31490.89820.35120.2959-0.8112-0.62521.1571-0.32070.6091-0.1085-0.17420.2428-0.16680.643441.849-13.76727.419
23.65884.3015-4.00915.4312-4.89054.47940.03390.2650.0541-0.17630.0182-0.02280.0893-0.1316-0.05210.5087-0.0005-0.27160.6606-0.17180.726549.023-16.94531.385
311.1094-7.13993.8485.4916-0.86484.2039-0.1214-0.16090.73070.22810.4846-0.84630.24570.621-0.36320.5786-0.0171-0.02760.34250.01730.647841.734-25.39623.517
41.79591.5271.71612.92810.65822.0404-0.0266-0.52310.26690.2659-0.25620.2885-0.2972-0.58830.28280.9140.1847-0.01370.4375-0.17510.432623.629-8.54416.47
50.1068-0.22150.15940.5201-0.69352.6567-0.1243-0.0665-0.08540.27660.12130.1639-0.1770.32670.0030.45360.03290.00380.17440.01620.383717.092-19.8780.715
63.1684-0.5250.10720.60720.66295.3947-0.20720.09240.08130.09170.050.0339-0.3248-0.42710.15720.4880.00080.00080.0730.00950.23727.576-15.203-2.076
71.4039-1.1399-0.68196.35941.20610.43420.02980.05740.13880.22040.0853-0.251-0.00480.0505-0.11510.41440.0028-0.02720.1766-0.03570.210420.216-26.25-13.663
80.8863-0.2699-0.29062.0493-0.582.54510.04170.12020.03290.00120.04840.20210.0308-0.2177-0.09010.40780.0231-0.00940.1147-0.00170.255915.479-37.317-16.926
90.7312-0.51250.02642.35890.58850.4034-0.0089-0.01330.1306-0.13550.0957-0.0912-0.13260.1586-0.08680.3781-0.0417-0.00290.1311-0.00410.235519.172-23.515-8.36
1011.2434-2.3302-5.32815.6504-0.52263.20690.23260.87890.89490.0964-0.3318-0.8574-0.2185-0.3760.09920.65070.0862-0.14580.5868-0.12910.631526.179-12.695-8.821
115.2947-3.3361-2.99927.472-1.01599.10490.0059-0.26970.30.2218-0.2254-0.0516-0.2248-0.07030.21950.51540.04840.03720.13490.06430.332547.042-66.186-57.413
123.4415-2.9246-0.33997.9566-1.89850.9183-0.2075-0.21540.0293-0.1167-0.0247-0.72740.14870.08570.23220.5367-0.0109-0.00360.21810.08730.266950.363-62.027-66.349
131.9023-2.7212-2.72323.89423.89763.903-0.0422-0.06020.0890.10840.106-0.09790.11180.0461-0.06380.87960.0581-0.02150.4472-0.10780.578831.291-33.886-60.93
143.6228-1.0397-0.7361.4540.40572.41060.1190.12160.034-0.03370.0730.1606-0.1998-0.1922-0.1920.3750.00150.00170.1235-0.00270.238415.188-18.777-47.793
154.31180.0605-0.93263.9175-0.83693.38620.02250.14280.0703-0.49170.09670.29670.39930.168-0.11920.34340.0047-0.02860.0894-0.05060.169519.511-27.67-49.241
162.2297-3.1558-1.60475.16761.09733.1983-0.3016-0.1284-0.00530.42370.139-0.08620.32730.06340.16260.3565-0.0499-0.02970.17690.0310.26520.042-26.648-37.293
172.6716-0.09361.11361.3066-0.20932.1806-0.0055-0.1766-0.1820.17450.12670.0530.04780.0655-0.12120.37070.02090.01030.1233-0.02980.2569-1.498-19.353-30.012
182.20860.54351.11730.79970.28024.2032-0.0733-0.10160.08340.05520.03090.1525-0.0786-0.05030.04230.36670.02450.03460.0809-0.04290.2834-3.053-13.525-36.361
193.2819-1.2764-1.48683.21761.62151.7553-0.0312-0.3190.0925-0.18760.04-0.2508-0.10710.3648-0.00880.3511-0.027-0.03590.1885-0.0090.222524.019-18.75-41.053
208.26570.1221-6.73468.6853-0.89619.470.1769-1.22550.668-0.3730.5721-0.6038-0.07681.2046-0.74910.4812-0.0643-0.09370.2516-0.15940.220725.579-12.248-38.035
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 55
3X-RAY DIFFRACTION3A56 - 67
4X-RAY DIFFRACTION4A68 - 92
5X-RAY DIFFRACTION5A93 - 112
6X-RAY DIFFRACTION6A113 - 155
7X-RAY DIFFRACTION7A156 - 169
8X-RAY DIFFRACTION8A170 - 232
9X-RAY DIFFRACTION9A233 - 294
10X-RAY DIFFRACTION10A295 - 303
11X-RAY DIFFRACTION11B1 - 43
12X-RAY DIFFRACTION12B44 - 81
13X-RAY DIFFRACTION13B82 - 92
14X-RAY DIFFRACTION14B93 - 112
15X-RAY DIFFRACTION15B113 - 137
16X-RAY DIFFRACTION16B138 - 160
17X-RAY DIFFRACTION17B161 - 229
18X-RAY DIFFRACTION18B230 - 263
19X-RAY DIFFRACTION19B264 - 295
20X-RAY DIFFRACTION20B296 - 305

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