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- PDB-4on0: Crystal Structure of NolR from Sinorhizobium fredii in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4on0
TitleCrystal Structure of NolR from Sinorhizobium fredii in complex with oligo AA DNA
Components
  • DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )
  • DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )
  • NolR
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / transcription regulator / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / 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
DNA / DNA (> 10) / NolR
Similarity search - Component
Biological speciesSinorhizobium fredii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, S.G. / Krishnan, H.B. / Jez, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.
Authors: Lee, S.G. / Krishnan, H.B. / Jez, J.M.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NolR
B: NolR
C: NolR
D: NolR
E: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )
G: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )
F: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )
H: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )


Theoretical massNumber of molelcules
Total (without water)77,9828
Polymers77,9828
Non-polymers00
Water00
1
A: NolR
B: NolR
E: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )
F: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )


Theoretical massNumber of molelcules
Total (without water)38,9914
Polymers38,9914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-52 kcal/mol
Surface area15410 Å2
MethodPISA
2
C: NolR
D: NolR
G: DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )
H: DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )


Theoretical massNumber of molelcules
Total (without water)38,9914
Polymers38,9914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-54 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.306, 131.306, 68.548
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
NolR


Mass: 12745.669 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium fredii (bacteria) / Gene: nolR / Production host: Escherichia coli (E. coli) / References: UniProt: Q83TD2
#2: DNA chain DNA (5 -D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)-3 )


Mass: 6774.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic
#3: DNA chain DNA (5 -D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)-3 )


Mass: 6725.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic

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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: 4.37 Å3/Da / Density % sol: 71.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG-3350, 0.1 M sodium citrate/citric acid, and 0.2 M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2013 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30.4 Å / Num. all: 23470 / Num. obs: 23470 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.054 / Net I/σ(I): 19.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OMY

4omy


Resolution: 3→30.38 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 963 4.99 %
Rwork0.185 --
obs0.187 19282 73.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 1762 0 0 4686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054900
X-RAY DIFFRACTIONf_angle_d0.8616958
X-RAY DIFFRACTIONf_dihedral_angle_d24.1811968
X-RAY DIFFRACTIONf_chiral_restr0.038816
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0029-3.16110.2325810.21671615X-RAY DIFFRACTION45
3.1611-3.35890.22621020.18711852X-RAY DIFFRACTION52
3.3589-3.61780.20471140.19362129X-RAY DIFFRACTION59
3.6178-3.98120.25971360.2112532X-RAY DIFFRACTION71
3.9812-4.55560.22771680.1813037X-RAY DIFFRACTION85
4.5556-5.73330.2011890.1853583X-RAY DIFFRACTION100
5.7333-30.38450.18051730.17223571X-RAY DIFFRACTION100
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)
18.2202-6.6393-4.75166.26474.87325.6656-0.5332-1.1877-0.3951.20520.58490.531-0.1058-0.1575-0.10170.88840.196-0.01660.66420.12430.3865-27.4818-20.69951.673
24.8566-0.4721-1.24387.769-0.03742.26130.3860.4681-1.1742-0.5485-0.1427-0.17240.70950.0718-0.30870.65480.2122-0.23290.4275-0.07970.575-9.9578-31.7671-13.704
31.58082.21590.10434.7463-2.02643.06230.53140.6065-0.4042-0.9159-0.4680.7298-0.0378-0.04710.15611.04010.0553-0.35390.4249-0.19551.0998-9.4489-40.4888-13.162
49.01431.6513.16575.67915.08386.25210.14660.8537-0.6868-1.23510.06170.85940.7228-0.6855-0.14240.71170.0925-0.31520.5244-0.2660.6203-25.8181-25.6903-17.464
53.3335-1.136-2.55871.74152.54914.03020.11490.9265-0.229-0.90990.0737-0.1580.31440.4426-0.05271.02780.1803-0.14840.7011-0.0530.1945-15.152-19.433-20.5408
63.8813-2.15760.28344.4478-0.47813.7402-0.3987-0.14420.57940.30770.2580.057-0.0298-0.4138-0.01410.39410.1909-0.22270.38870.16350.4248-29.3522-6.6958-3.4214
72.9405-2.8882-0.20135.84071.26371.7321-0.07430.1687-0.44980.09570.15550.6088-0.0111-0.3488-0.2130.44050.0397-0.25790.48610.18510.6927-32.9523-13.4692-8.9904
85.3137-2.7994-1.6013.27391.99813.21460.020.2375-0.7144-0.4235-0.26990.61020.36150.00230.44441.12540.56150.23550.3228-0.04880.62811.3271-30.9408-3.7138
92.6996-2.8510.31853.2204-1.09692.8647-0.3321-0.06351.15770.68140.2578-0.4670.14860.42530.01610.64710.2244-0.31350.4121-0.0521.0119-0.4374-12.6137-4.0055
104.4479-3.3344-0.37065.0951-0.89640.5803-0.6627-0.53811.22490.83930.5626-0.2053-0.5843-0.12880.03630.83030.4987-0.46630.5434-0.0610.8524-20.86824.77621.9728
115.0476-4.85770.66727.4857-3.70523.4284-1.0151-1.13860.58732.38330.5412-0.3585-1.1429-0.08170.34551.29130.4513-0.22980.5560.04420.9273-30.441211.54265.1018
128.542-2.83895.63020.9439-1.87063.8376-0.1130.26030.15090.3217-0.2893-0.6708-0.12960.56720.42110.52070.2056-0.42490.6449-0.0010.982-15.30213.2314-0.0478
131.3722-0.5892-0.08912.1711-0.56640.2404-0.4571-0.28560.47790.19540.1136-0.35650.13310.0920.11270.62160.2755-0.21480.46680.02240.5365-2.6208-16.8745-2.4683
1424.8639-1.33895.20851.37471.54990.01571.1971-0.5279-2.26440.009-1.2956-0.85212.0845-0.05051.36960.27130.25671.29020.06560.489217.9162-26.2624-7.3876
152.8915-2.8406-1.30423.27391.69530.9514-0.9273-1.49860.51180.75630.13010.4101-0.1092-0.52180.71980.56130.2390.05891.47860.07010.8765-59.55378.7013-5.8901
162.3243-0.9242-1.22220.70590.53090.6686-0.12240.705-0.7772-0.3724-0.01570.25490.1709-0.0227-0.06160.258-0.0318-0.15410.84380.18540.6351-43.5577-3.1867-24.7631
172.2768-1.36881.81931.4-0.7812.8951-0.2222-0.11080.16610.11430.212-0.0488-0.04640.20150.11280.3363-0.0397-0.37070.58960.2460.6451-42.48116.9142-21.8429
184.14530.55371.32311.7281-0.92934.63140.182-0.4547-0.8129-0.04010.08520.00920.3531-0.6896-0.22780.27010.0617-0.27270.66010.36890.6395-43.0573-4.0612-16.3523
190.78760.5757-0.94682.1232-1.38261.70060.10980.5657-1.3942-0.32710.1498-0.1890.69370.5263-0.22050.74220.202-0.41251.37380.05451.1639-45.9973-9.8183-33.8695
208.7854-3.10773.57823.6891-2.0321.91020.19481.356-0.2352-0.4487-0.34340.0894-0.19290.13390.09540.4202-0.0382-0.27751.19670.26830.7078-57.8822-3.0036-25.1673
212.00040.25670.32611.37471.44351.5157-0.3572-1.4797-0.97020.53520.31420.35850.2527-0.106-0.01950.430.06090.03721.56010.58350.9443-67.13185.4161-9.7116
224.7757-0.12370.43674.6484-0.68098.6778-0.4435-1.0591-0.2360.7592-0.54681.18660.4171-0.30130.85560.5142-0.00070.13531.86320.45861.222-75.183310.4699-7.3926
236.1189-1.20072.54562.94520.00911.15260.0362-0.1459-0.45830.19770.42960.55170.2369-0.4069-0.43650.3411-0.0324-0.20711.33680.45291.0209-74.86036.39-17.8143
240.78230.73791.08080.69581.01911.490.08440.112-0.308-0.2636-0.00650.5709-0.3418-0.4868-0.04490.5916-0.1135-0.20531.63370.57551.3408-80.83183.6239-12.7828
259.3233-3.96430.77797.0037-0.98518.7096-0.2123-0.791-0.34290.66410.04560.53120.5539-0.70130.22110.47790.17540.13371.10210.33960.8358-60.0902-3.8932-7.9314
262.19460.0698-0.29382.9776-1.13882.2409-0.13920.11530.25130.02810.8407-0.1220.2303-0.2323-0.24090.22130.1232-0.16911.23810.38871.1542-45.498915.9772-29.4291
272.7093-0.81310.11660.26470.06190.39790.0685-0.16460.1499-0.05510.12470.56210.0052-0.59530.09080.29140.39040.00981.88870.31981.5618-78.603918.4063-21.3717
284.10771.00982.32251.02560.01025.4473-0.6935-0.78720.56910.23280.20340.2799-0.3436-0.61790.30930.47730.2154-0.06392.00190.23191.6283-89.305618.6702-15.601
299.28253.76410.31792.31390.96170.8947-0.07470.83910.9623-0.32780.34560.2415-0.15290.2227-0.16640.42620.0073-0.06331.57130.58611.449-74.532418.7504-25.9359
306.0882-2.3386-1.10992.64071.02590.4448-0.0391-0.12491.0306-0.09850.4992-0.0696-0.2009-0.3419-0.27950.1890.1437-0.20941.11880.35371.3432-57.858421.4592-23.1362
313.14510.24531.42031.23990.52540.7837-0.03880.24770.0911-0.050.2713-0.11960.05950.12240.11010.1865-0.1069-0.25911.12460.20280.6865-43.907812.7403-33.6969
322.05270.6929-0.58010.2337-0.19570.1639-0.39390.9860.2351-0.4240.39890.14940.5453-0.37330.01720.8799-0.017-0.42321.4042-0.42690.8997-32.826919.7137-42.8156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 102 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 102 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 10 )
10X-RAY DIFFRACTION10chain 'E' and (resid 11 through 22 )
11X-RAY DIFFRACTION11chain 'F' and (resid 2 through 6 )
12X-RAY DIFFRACTION12chain 'F' and (resid 7 through 11 )
13X-RAY DIFFRACTION13chain 'F' and (resid 12 through 21 )
14X-RAY DIFFRACTION14chain 'F' and (resid 22 through 22 )
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 26 )
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 55 )
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 69 )
18X-RAY DIFFRACTION18chain 'C' and (resid 70 through 102 )
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 10 )
20X-RAY DIFFRACTION20chain 'D' and (resid 11 through 26 )
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 40 )
22X-RAY DIFFRACTION22chain 'D' and (resid 41 through 55 )
23X-RAY DIFFRACTION23chain 'D' and (resid 56 through 77 )
24X-RAY DIFFRACTION24chain 'D' and (resid 78 through 87 )
25X-RAY DIFFRACTION25chain 'D' and (resid 88 through 102 )
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 10 )
27X-RAY DIFFRACTION27chain 'G' and (resid 11 through 22 )
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 6 )
29X-RAY DIFFRACTION29chain 'H' and (resid 7 through 11 )
30X-RAY DIFFRACTION30chain 'H' and (resid 12 through 16 )
31X-RAY DIFFRACTION31chain 'H' and (resid 17 through 21 )
32X-RAY DIFFRACTION32chain 'H' and (resid 22 through 22 )

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