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- PDB-3k1m: Crystal Structure of full-length BenM, R156H mutant -

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Basic information

Entry
Database: PDB / ID: 3k1m
TitleCrystal Structure of full-length BenM, R156H mutant
ComponentsHTH-type transcriptional regulator benM
KeywordsTRANSCRIPTION / HTH / LysR-type transcripational regulator / Activator / Aromatic hydrocarbons catabolism / DNA-binding / Transcription regulation
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 / 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 / molecular replacement / Resolution: 2.29 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 / Derived calculations / Category: database_2 / 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
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:
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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)71,6458
Polymers71,2522
Non-polymers3936
Water9,152508
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)143,29016
Polymers142,5044
Non-polymers78712
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 area12060 Å2
ΔGint-103 kcal/mol
Surface area56750 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)143,29016
Polymers142,5044
Non-polymers78712
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 area10200 Å2
ΔGint-93 kcal/mol
Surface area58620 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)71,6458
Polymers71,2522
Non-polymers3936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z+1/21
Buried area3770 Å2
ΔGint-41 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.997, 70.789, 186.275
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: 35625.984 Da / Num. of mol.: 2 / Mutation: R156H
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 62.02 %
Crystal growTemperature: 295 K / Method: microbatch under oil
Details: 5mcL precipitant and 4 mcL protein solution. Precipitant: 80% Crystal Screen 2 (CS-2, Hampton Research) condition 31, 20% CS-2 condition 26 Protein: 30 mM Tris, 0.5 M NaCl, 10% glycerol, 250 ...Details: 5mcL precipitant and 4 mcL protein solution. Precipitant: 80% Crystal Screen 2 (CS-2, Hampton Research) condition 31, 20% CS-2 condition 26 Protein: 30 mM Tris, 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM mercaptolethanol, pH 9.0, MICROBATCH UNDER OIL, temperature 295K

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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 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.614
11K, H, -L20.386
ReflectionResolution: 2.29→100 Å / Num. obs: 41907 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 25.981 Å2 / Rmerge(I) obs: 0.071 / Χ2: 2.113 / Net I/σ(I): 13.7
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.81 / Num. unique all: 2078 / Rsym value: 0.507 / Χ2: 1.325 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.98 Å48.27 Å
Translation2.98 Å48.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F97

2f97


Resolution: 2.29→49.77 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.181 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.04 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : RESIDUAL ONLY Twin refinement performed with two domains, twin fraction 0.614
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2116 5.1 %RANDOM
Rwork0.147 ---
all0.148 41729 --
obs0.148 41729 97.84 %-
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: 80.54 Å2 / Biso mean: 25.981 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-9.18 Å20 Å20 Å2
2--15.41 Å20 Å2
3----24.59 Å2
Refinement stepCycle: LAST / Resolution: 2.29→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 24 508 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225030
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9836821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77523.947228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94215915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2671534
X-RAY DIFFRACTIONr_chiral_restr0.0680.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213764
X-RAY DIFFRACTIONr_mcbond_it1.98763055
X-RAY DIFFRACTIONr_mcangle_it2.74684976
X-RAY DIFFRACTIONr_scbond_it0.95631975
X-RAY DIFFRACTIONr_scangle_it1.3694.51835
LS refinement shellResolution: 2.29→2.343 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 117 -
Rwork0.196 2011 -
all-2128 -
obs--69.59 %
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)
113.0821-6.51836.684815.9875-0.63384.4028-0.6133-0.17660.77090.54140.7906-1.6101-0.17180.1453-0.17720.2402-0.1556-0.22460.4315-0.16150.758141.174-13.90127.806
29.79176.89440.148814.3864-1.49114.91040.8296-0.6940.64310.355-0.2191-0.9324-0.52421.2348-0.61050.3114-0.179-0.1150.8481-0.32621.037147.736-15.04931.498
320.54441.22889.08254.4027-2.037913.94880.5444-1.1447-0.48770.6372-0.6547-1.7358-0.27242.00740.11030.24860.0988-0.31321.1399-0.14131.566551.149-25.40127.346
47.183-2.64231.672311.8446-5.72483.73280.40430.51360.2293-0.8225-0.5767-0.88490.22430.65420.17240.2938-0.15360.08230.3847-0.10290.479738.797-23.27422.206
56.8932-8.14333.015712.6633-4.56395.06250.37890.2399-0.2513-0.8155-0.2523-0.0063-0.6418-0.0036-0.12660.5298-0.07780.02390.2642-0.06430.356927.786-9.01418
68.4355-2.4977-1.098721.875812.373315.773-0.4114-1.28411.40121.51180.2741-0.2068-0.3909-0.29610.13730.97130.0637-0.03060.3768-0.23220.54159.332-5.75511.042
73.7307-0.8583-0.18652.3946-0.02393.1035-0.0766-0.2420.14440.33270.0049-0.0696-0.109-0.05910.07170.2852-0.0152-0.0050.12170.03810.226413.863-18.0132.291
82.7793-0.63910.30392.51080.04745.57620.00840.22780.0226-0.0574-0.13560.2472-0.3553-0.78020.12710.19620.0209-0.01180.15630.0170.17964.747-15.083-7.477
91.7236-2.9273-0.43078.50971.19591.71420.17670.20560.2313-0.346-0.2404-0.616-0.12080.14820.06370.15880.00070.0130.17010.03430.204323.809-31.79-15.007
101.027-0.0140.11012.6918-1.75793.71460.03870.1684-0.1045-0.18640.0780.38780.1272-0.3639-0.11660.17950.0104-0.00250.12880.01680.251812.983-37.176-15.939
111.8884-1.02520.66453.2086-1.13684.6640.02320.0963-0.0144-0.0875-0.0975-0.09550.01240.17940.07430.16590.00530.03420.13310.02920.229623.517-37.684-10.033
123.6451-1.8478-3.70053.20663.61975.55760.13720.25580.0258-0.4123-0.32270.1363-0.3896-0.27670.18560.29850.0116-0.04290.18170.06860.189614.121-17.441-13.568
137.7142-6.8385-1.32017.81071.89021.79530.12050.37830.8072-0.1513-0.007-0.6548-0.5370.2207-0.11350.4117-0.1546-0.02950.21940.08350.283418.692-7.766-2.577
1431.006-1.3182-7.099121.447-6.223922.78350.06640.88461.0761-1.1948-0.6487-0.8587-0.6799-0.25440.58230.47130.0238-0.12530.3583-0.16380.512829.706-15.703-6.974
1513.37276.69037.686218.9697-1.57618.11-0.81523.27782.43951.2734-0.71960.54250.61854.3581.53482.39051.0804-0.01232.67880.72632.674419.421-5.44-9.947
164.3175-1.6428-0.015310.195-3.45386.74410.1795-0.30360.33371.0711-0.0884-0.046-0.5660.2293-0.09110.5072-0.01120.11490.19320.03990.328248.634-63.811-57.564
173.2352-0.55770.011511.7338-0.58138.09720.11-0.44640.18981.36780.09840.5705-0.492-0.058-0.20840.51090.01570.16450.23070.06980.330145.787-68.881-54.074
186.00043.04080.291412.4751-0.34975.29370.261-0.2724-0.75320.0045-0.2758-0.47930.61720.20440.01480.5451-0.02030.06940.2890.11760.356751.43-73.107-63.387
194.651-1.2085-0.081311.6597-0.97144.21580.22370.36960.136-0.7019-0.4095-0.58240.2450.33990.18580.4122-0.05260.09890.32350.11750.275551.538-62.239-67.807
209.32341.265-1.947217.4271-2.129512.8537-0.0695-0.79060.57160.69850.20781.0763-0.713-0.5967-0.13830.291-0.08330.04280.33430.0240.23937.725-43.683-64.311
2112.4063-1.0232-2.561610.6822-0.26188.27220.14181.1637-0.5257-1.2159-0.1985-1.08220.31840.7510.05670.23930.0360.03990.3498-0.05180.267324.944-28.524-55.04
223.7974-0.74960.48184.0924-1.06542.574-0.12410.4104-0.0194-0.17370.07390.02820.09940.1710.05010.1661-0.0289-0.01660.196-0.01640.139317.154-22.813-48.478
234.6886-2.0228-0.76342.3053-0.87655.4001-0.274-0.0036-0.22260.24160.08110.03060.40130.25060.19290.18230.01330.02870.13590.01690.175620.474-30.238-38.297
249.8928-2.4934-0.32181.90850.05451.386-0.2925-0.64830.5830.26120.2065-0.0219-0.36870.0220.08590.28830.0138-0.04540.1273-0.01840.18251.89-11.269-31.157
253.57310.51811.51591.7275-0.63613.07130.0498-0.1719-0.41840.10390.02910.12450.2253-0.1438-0.07890.18980.033-0.01520.14950.01880.24180.154-22.646-28.701
262.44421.22322.12871.64011.95047.42860.2227-0.3021-0.4170.2629-0.05590.06130.6486-0.5536-0.16680.19620.0389-0.01770.15970.09470.3516-2.407-25.842-27.463
278.1344-2.32541.15216.10631.05555.5965-0.1915-0.0117-0.53640.15110.12050.42020.3422-0.24980.0710.2332-0.06080.03550.1412-0.06040.2412-7.438-20.104-39.657
281.2385-0.1339-0.4130.70070.10190.7606-0.1606-0.05530.08990.09570.04320.0755-0.14020.05130.11740.17450.016-0.02750.1123-0.00880.15133.973-14.194-34.668
295.5823-1.6304-1.60375.5679-0.08883.5453-0.09830.01080.14210.08210.044-0.6514-0.12350.51950.05420.0996-0.0341-0.01810.27590.00390.178227.592-19.235-43.665
306.4425-4.5196-3.47998.63253.23713.33660.0029-0.33360.3201-0.3260.2261-0.768-0.10970.6747-0.2290.33040.0045-0.00530.4362-0.01810.280924.77-10.962-38.961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 47
3X-RAY DIFFRACTION3A48 - 61
4X-RAY DIFFRACTION4A62 - 68
5X-RAY DIFFRACTION5A69 - 86
6X-RAY DIFFRACTION6A87 - 92
7X-RAY DIFFRACTION7A93 - 132
8X-RAY DIFFRACTION8A133 - 154
9X-RAY DIFFRACTION9A155 - 180
10X-RAY DIFFRACTION10A181 - 237
11X-RAY DIFFRACTION11A238 - 261
12X-RAY DIFFRACTION12A262 - 276
13X-RAY DIFFRACTION13A277 - 294
14X-RAY DIFFRACTION14A295 - 299
15X-RAY DIFFRACTION15A300 - 304
16X-RAY DIFFRACTION16B1 - 22
17X-RAY DIFFRACTION17B23 - 40
18X-RAY DIFFRACTION18B41 - 54
19X-RAY DIFFRACTION19B55 - 73
20X-RAY DIFFRACTION20B74 - 87
21X-RAY DIFFRACTION21B88 - 94
22X-RAY DIFFRACTION22B95 - 135
23X-RAY DIFFRACTION23B136 - 155
24X-RAY DIFFRACTION24B156 - 180
25X-RAY DIFFRACTION25B181 - 212
26X-RAY DIFFRACTION26B213 - 225
27X-RAY DIFFRACTION27B226 - 239
28X-RAY DIFFRACTION28B240 - 273
29X-RAY DIFFRACTION29B274 - 294
30X-RAY DIFFRACTION30B295 - 305

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