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- PDB-5l10: Crystal Structure of N-Acylhomoserine Lactone Dependent LuxR Fami... -

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Basic information

Entry
Database: PDB / ID: 5l10
TitleCrystal Structure of N-Acylhomoserine Lactone Dependent LuxR Family Transcriptionl Factor CepR2 from Burkholderia cenocepacia
ComponentsN-acylhomoserine lactone dependent regulatory protein
KeywordsTRANSCRIPTION / CepR2 / transcription factor / ligand binding domain / alpha-beta structure / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / N-acylhomoserine lactone dependent regulatory protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsKim, Y. / Chhor, G. / Jedrzejczak, R. / Winan, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of N-Acylhomoserine Lactone Dependent LuxR Family Transcriptionl Factor CepR2 from Burkholderia cenocepacia.
Authors: Kim, Y. / Chhor, G. / Jedrzejczak, R. / Winan, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylhomoserine lactone dependent regulatory protein
B: N-acylhomoserine lactone dependent regulatory protein
C: N-acylhomoserine lactone dependent regulatory protein
D: N-acylhomoserine lactone dependent regulatory protein
E: N-acylhomoserine lactone dependent regulatory protein
F: N-acylhomoserine lactone dependent regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,08719
Polymers116,1516
Non-polymers93713
Water1,802100
1
A: N-acylhomoserine lactone dependent regulatory protein
B: N-acylhomoserine lactone dependent regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0857
Polymers38,7172
Non-polymers3685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-15 kcal/mol
Surface area15070 Å2
MethodPISA
2
C: N-acylhomoserine lactone dependent regulatory protein
D: N-acylhomoserine lactone dependent regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0857
Polymers38,7172
Non-polymers3685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-19 kcal/mol
Surface area14690 Å2
MethodPISA
3
E: N-acylhomoserine lactone dependent regulatory protein
F: N-acylhomoserine lactone dependent regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9175
Polymers38,7172
Non-polymers2003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-11 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.276, 74.594, 118.027
Angle α, β, γ (deg.)90.00, 117.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acylhomoserine lactone dependent regulatory protein / N-Acylhomoserine Lactone Dependent LuxR Family Transcription Factor CepR2


Mass: 19358.430 Da / Num. of mol.: 6 / Fragment: UNP residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM0188 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: B4EHM0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.09 Å3/Da / Density % sol: 69.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium formate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 48922 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.6
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 1.87 / CC1/2: 0.749 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→40.67 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.99
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 2158 5.02 %random
Rwork0.1821 ---
obs0.1838 43030 87.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.8 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 61 100 8015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048206
X-RAY DIFFRACTIONf_angle_d0.66111179
X-RAY DIFFRACTIONf_dihedral_angle_d15.7074810
X-RAY DIFFRACTIONf_chiral_restr0.0431171
X-RAY DIFFRACTIONf_plane_restr0.0061469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7413-2.80510.2868610.27391190X-RAY DIFFRACTION39
2.8051-2.87520.3025900.27151545X-RAY DIFFRACTION50
2.8752-2.95290.30661280.24691983X-RAY DIFFRACTION65
2.9529-3.03980.28611270.22992371X-RAY DIFFRACTION77
3.0398-3.13790.25851510.23292794X-RAY DIFFRACTION90
3.1379-3.250.24511580.23613023X-RAY DIFFRACTION98
3.25-3.38010.24241680.22163085X-RAY DIFFRACTION100
3.3801-3.53380.24851360.19413127X-RAY DIFFRACTION100
3.5338-3.720.19711560.18263090X-RAY DIFFRACTION100
3.72-3.95290.2141680.17433084X-RAY DIFFRACTION100
3.9529-4.25780.19851590.15513118X-RAY DIFFRACTION100
4.2578-4.68570.16851690.13673101X-RAY DIFFRACTION99
4.6857-5.36240.17821720.14433118X-RAY DIFFRACTION100
5.3624-6.75110.23611760.18463110X-RAY DIFFRACTION100
6.7511-40.67460.20071390.16873133X-RAY DIFFRACTION96
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)
18.6952-3.1907-3.34593.49223.51173.8991-0.0370.86860.2931-0.5287-0.2556-0.4409-0.5927-0.0059-0.02390.43450.00210.05840.33320.03260.33887.2286-5.35287.8485
24.32650.5867-0.06753.7744-0.02183.25420.04430.01870.30530.12240.00910.4035-0.086-0.178-0.06830.2128-0.00870.00830.1095-0.01950.1852-6.3044-6.243692.4176
33.20453.10541.30696.55141.04352.31240.60630.890.6405-0.61240.22490.19230.6009-0.55220.21790.55190.07590.38510.90540.15930.8643-17.8158-12.5799110.0418
45.08291.4858-1.66970.71050.91127.4869-0.1671-0.07630.2308-0.0518-0.27820.05830.0356-0.77380.2680.29980.063-0.00350.2622-0.02560.5526-19.7826-7.248593.2246
55.4189-1.20861.49171.71520.84213.7209-0.4414-0.2185-1.5310.22760.14340.64191.0241-0.5686-0.28550.312-0.1747-0.04910.3061-0.05230.4387-15.6167-21.632992.9489
63.9929-0.3249-0.08762.31870.91825.24720.09550.0442-0.4912-0.3761-0.06050.4510.149-0.31970.00090.2528-0.0055-0.08550.1112-0.03610.3437-12.5486-15.912189.9462
75.3733-1.6355-1.07476.33351.83964.94010.1806-0.0428-0.0538-0.2250.1706-0.0352-0.10570.6798-0.39650.21940.0182-0.07010.15250.0610.2074-0.8392-11.769494.4612
85.9691-3.18221.72639.6424-1.3318.68860.25781.45730.1598-1.93260.1245-0.84260.48870.5862-0.18480.54960.02540.01190.4967-0.02270.364610.7762-21.468786.0496
95.83960.0179-0.06435.0074-1.71686.16430.3760.3378-0.1507-0.42330.16250.15810.56280.4139-0.25720.20060.012-0.01440.1855-00.204313.4579-25.881998.5284
103.0449-1.24240.36145.26134.71385.09340.09960.18080.19570.72910.2177-0.112-0.02260.6977-0.35020.94220.14960.17690.96680.30790.84013.4759-25.6893120.2109
113.3296-1.07861.66133.8934-1.26064.0867-0.0891-0.15390.17360.34570.0667-0.3557-0.19760.24360.00590.205-0.0041-0.01340.1657-0.01660.204316.2705-17.2599109.818
128.14323.80061.76732.788-0.24476.5372-0.10170.59960.0418-0.65950.2504-0.41190.16870.3687-0.0560.2590.02090.05140.23710.07920.260910.6599-13.903995.2584
134.3682-4.8006-4.43838.43377.03215.9970.0041-0.1549-0.75220.882-0.3341.78191.1437-1.5431-0.0020.4573-0.2044-0.1560.45910.15540.59182.5264-30.1482103.8581
148.97932.00881.1042.59512.88519.5781-0.31880.07880.6439-0.1873-0.20211.2879-1.2456-1.65570.37820.47720.1193-0.12380.6809-0.09130.4996-43.428-9.010947.2958
158.0331-1.16420.82055.23811.40125.3783-0.4129-0.46051.05450.10690.0087-0.1692-1.30860.17020.30440.3306-0.0224-0.15310.3198-0.03830.3513-31.979-6.945954.5256
162.28830.2234-3.11885.8635-0.92074.3724-0.42140.1015-0.7046-0.3993-0.0165-1.3889-0.49990.8573-0.20130.4745-0.0452-0.13070.6458-0.15680.5741-18.8182-8.608758.1095
172.69460.54580.10433.561-1.00334.3185-0.1191-0.1884-0.00680.49010.1627-0.7367-0.48350.6314-0.0810.2893-0.0458-0.08610.4073-0.00740.2712-20.1791-13.507665.6487
183.36810.21150.04763.6961-0.10716.4177-0.25470.1238-0.16070.18930.2865-0.10010.3191-0.07480.07920.1391-0.0378-0.04470.2955-0.06840.1826-28.407-18.831562.7245
195.62041.43811.34647.2596-0.88797.5569-0.47910.60650.0961-0.11330.45330.0161-0.2725-0.3765-0.09260.2589-0.0033-0.01960.3668-0.07030.1528-33.2722-15.163750.6664
203.8532-5.2734-3.48218.96754.03644.35240.5613-0.3118-0.44080.1335-0.46041.75060.4783-0.8255-0.00610.2918-0.1830.07950.7022-0.00290.4682-43.7388-27.065447.3254
214.0874-0.45410.51135.4781-0.22084.81640.20460.3016-0.2025-0.02160.02510.00830.3240.0067-0.19720.2646-0.0484-0.05020.33460.03730.1688-34.9496-28.804936.5142
224.03830.64085.01375.47260.20026.38480.66931.0588-0.1695-0.1089-0.2086-1.44760.83181.2267-0.50420.4453-0.01340.0670.5073-0.20660.4783-22.8896-28.991330.6565
233.6336-2.6673-0.50212.5271.04466.60530.02370.1790.2096-0.21810.1012-0.1316-0.36580.7829-0.07570.3185-0.14330.03010.37820.03640.2469-27.9836-20.408825.283
243.6107-0.34311.91142.93290.7427.6916-0.03110.18230.0179-0.27770.1747-0.0367-0.17870.2865-0.10250.2115-0.0583-0.0160.2201-0.00610.1863-32.4916-19.388727.9728
255.6523-2.52051.3983.088-2.51798.1632-0.1253-0.6515-0.2237-0.28710.28450.44810.1958-0.3264-0.20560.1966-0.0908-0.04240.297-0.060.2336-34.6637-20.906641.0197
269.2754-1.3113-3.01517.510.98546.3317-0.2026-1.80420.80141.65230.2621-0.4673-0.48720.88080.12681.0806-0.12430.21330.6842-0.12750.5319-53.0049-11.7287108.3632
276.1571-0.08981.56413.5357-0.07744.07020.66020.26770.573-0.0333-0.09860.1869-0.64210.165-0.45080.7117-0.14610.2290.27260.02720.4594-51.0959-9.345291.4584
285.6931-1.0637-0.71081.9264-0.47524.48550.31110.2985-0.27810.0134-0.2898-0.1055-0.05280.39790.00350.3521-0.08290.04890.3706-0.0190.3317-43.9142-18.753486.0436
299.3167-3.7620.70117.5188-1.26595.66640.32780.1190.24630.4754-0.4028-0.226-0.6521-0.13810.15730.4754-0.14180.21650.21340.01510.392-53.4309-17.502997.7159
303.1429-0.28022.81776.1539-2.53963.44870.4023-1.6893-1.2181.1677-0.2928-0.432-0.7790.4302-0.17360.9681-0.25860.11210.74270.1730.7102-52.2238-27.2007110.6289
312.81960.65830.74984.7438-0.26575.19610.2958-0.1966-1.19220.1407-0.0788-0.48340.3477-0.0576-0.14640.4256-0.0834-0.00190.22850.02440.6708-63.4835-32.5003105.2637
324.49740.2205-0.99091.9241.08180.9502-0.19110.6262-0.5396-0.4005-0.21780.62950.2037-0.1818-0.18210.5275-0.1443-0.14220.07480.03371.0181-74.0697-33.28696.7284
336.03640.2484-1.90431.42690.82835.8860.47640.2583-0.14330.0298-0.2123-0.0279-0.3978-0.3418-0.28710.46450.0010.07280.14720.03360.3494-72.3816-24.1489103.6934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 99 )
6X-RAY DIFFRACTION6chain 'A' and (resid 100 through 139 )
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 14 )
9X-RAY DIFFRACTION9chain 'B' and (resid 15 through 43 )
10X-RAY DIFFRACTION10chain 'B' and (resid 44 through 52 )
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 139 )
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 168 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 14 )
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 44 )
16X-RAY DIFFRACTION16chain 'C' and (resid 45 through 60 )
17X-RAY DIFFRACTION17chain 'C' and (resid 61 through 84 )
18X-RAY DIFFRACTION18chain 'C' and (resid 85 through 139 )
19X-RAY DIFFRACTION19chain 'C' and (resid 140 through 167 )
20X-RAY DIFFRACTION20chain 'D' and (resid 0 through 15 )
21X-RAY DIFFRACTION21chain 'D' and (resid 16 through 44 )
22X-RAY DIFFRACTION22chain 'D' and (resid 45 through 60 )
23X-RAY DIFFRACTION23chain 'D' and (resid 61 through 95 )
24X-RAY DIFFRACTION24chain 'D' and (resid 96 through 139 )
25X-RAY DIFFRACTION25chain 'D' and (resid 140 through 167 )
26X-RAY DIFFRACTION26chain 'E' and (resid -1 through 14 )
27X-RAY DIFFRACTION27chain 'E' and (resid 15 through 60 )
28X-RAY DIFFRACTION28chain 'E' and (resid 61 through 139 )
29X-RAY DIFFRACTION29chain 'E' and (resid 140 through 167 )
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 14 )
31X-RAY DIFFRACTION31chain 'F' and (resid 15 through 43 )
32X-RAY DIFFRACTION32chain 'F' and (resid 44 through 60 )
33X-RAY DIFFRACTION33chain 'F' and (resid 61 through 167 )

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