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- PDB-7d98: Crystal structure of full-length CbnR complexed with the target D... -

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Basic information

Entry
Database: PDB / ID: 7d98
TitleCrystal structure of full-length CbnR complexed with the target DNA complex
Components
  • (DNA (56-mer)) x 2
  • LysR-type regulatory protein
KeywordsDNA BINDING PROTEIN/DNA / LysR-type regulatory protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / LysR-type regulatory protein
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSenda, M. / Giannopoulou, E. / Senda, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06098 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA.
Authors: Giannopoulou, E.A. / Senda, M. / Koentjoro, M.P. / Adachi, N. / Ogawa, N. / Senda, T.
History
DepositionOct 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: LysR-type regulatory protein
B: LysR-type regulatory protein
P: LysR-type regulatory protein
Q: LysR-type regulatory protein
G: DNA (56-mer)
H: DNA (56-mer)


Theoretical massNumber of molelcules
Total (without water)162,8506
Polymers162,8506
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-132 kcal/mol
Surface area55170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.819, 105.819, 602.516
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein
LysR-type regulatory protein


Mass: 32085.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: cbnR, BJN34_37375 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WXC7
#2: DNA chain DNA (56-mer)


Mass: 17319.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cupriavidus necator (bacteria)
#3: DNA chain DNA (56-mer)


Mass: 17190.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cupriavidus necator (bacteria)

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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: 2.99 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20%(w/v) PEG 3350, 0.5%(w/v) n-Octyl-pyranoside, 4%(v/v) Tacsimate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 13, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. obs: 23984 / % possible obs: 98.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 116.8 Å2 / Rpim(I) all: 0.061 / Net I/σ(I): 12
Reflection shellResolution: 3.6→3.89 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4793 / Rpim(I) all: 0.458

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Processing

Software
NameVersionClassification
XDSdata processing
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.18.2-3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IZ1

1iz1


Resolution: 3.6→20 Å / SU ML: 0.5551 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2861 1187 4.95 %
Rwork0.2344 22773 -
obs0.237 23960 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.84 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8088 1170 0 0 9258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049560
X-RAY DIFFRACTIONf_angle_d0.706113291
X-RAY DIFFRACTIONf_chiral_restr0.04471603
X-RAY DIFFRACTIONf_plane_restr0.00631526
X-RAY DIFFRACTIONf_dihedral_angle_d20.80961760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.760.36731270.33312740X-RAY DIFFRACTION97.48
3.76-3.960.38021380.29592755X-RAY DIFFRACTION97.8
3.96-4.210.29621620.26572754X-RAY DIFFRACTION97.98
4.21-4.530.261450.22262784X-RAY DIFFRACTION98.35
4.53-4.980.28541510.20942819X-RAY DIFFRACTION98.64
4.98-5.680.29761440.23882860X-RAY DIFFRACTION98.78
5.68-7.10.30071440.24562950X-RAY DIFFRACTION99.29
7.1-200.25091760.20083111X-RAY DIFFRACTION99.31
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)
11.599916573451.168926608220.6801924822934.06138581536-3.374581201794.86871583318-0.5074001127890.0827633782156-0.212498875206-1.007895600290.538810163744-0.0864965633177-0.00685275791722-1.12740514397-0.0175205123911.33304613135-0.2512918448640.1187757657771.18211092537-0.07272721904261.13238749962-22.1646111271-18.3663603187-50.260525693
22.259940121281.06647710439-1.396365461462.22179189686-0.3777748670425.05031139241-0.145679856020.00865178079095-0.19093654806-0.335669723410.0545688514752-0.2093000624150.02836707431360.2459975485840.05293854011970.7950001831010.0225227855091-0.02291012497010.55445629552-0.0318237670140.793209255281-2.83752519679-17.293809297-23.1009723239
34.14422500954-0.807054198719-0.3047557492775.5444791673-1.156924320762.944888916210.222607441171-0.3583242346110.0417111238961-0.4871264605840.08606395474750.2127785932740.163462349880.472692963891-0.08018114434420.758655484787-0.0313138676844-0.1681240699260.570946861839-0.055918508630.759858630566-14.4248760955-14.4502635316-10.776056858
43.141047462420.967386911321-1.601636017321.62715980486-0.5470011885295.21121589764-0.1029574732010.0841505587513-0.0413716934368-0.3095629649990.072325152251-0.439929562038-0.159560105551-0.01166874440750.04699065463940.7765934081040.00835897394834-0.03162228938690.5606533466670.02348421991110.8835257584522.91668662537-15.8609713287-23.5790937153
56.326633052391.79842713414-1.399502998673.10884257257-1.50687550470.918880098454-1.222520860830.187543745279-0.584847411255-0.5766600594520.549602597809-0.432699080393-0.1884861338981.017850268990.4880574676821.84177847411-0.7620352438190.1851502622541.53605407335-0.07014046337060.969934617128-6.29529909779-19.9535106977-67.8183631484
64.5785979151-1.630026679990.9720498181361.417841246711.98297027147.275171718311.41017929719-0.812699550053-0.2407665098070.43387361033-0.949480608575-0.392041981173-0.291042264712-0.127281819712-0.2537914178591.74421477386-0.392018680059-0.1844486899531.05586417943-0.05118508978960.999866947193-11.1376645874-28.0664935697-52.9480299411
72.596108254261.57810178106-1.55845548683.81306977433-1.230766266254.17233594445-0.3370444516040.519601287074-0.134131198306-0.3336416852470.4545081101810.2580477923210.214413662569-0.723193557494-0.02099541348120.708358310047-0.104274309949-0.08530757384390.741189196607-0.02755103541360.780402988882-35.2134212887-46.3656254358-17.582537011
82.49132120280.742749988311-3.74772360388.97791649288-4.215105215216.8880599313-0.449826319146-0.04632079392021.16004908115-0.7577485513791.367253527621.191832620051.72606337606-1.01115130235-0.4771974614941.08463159399-0.318064599003-0.1721716644081.50361704491-0.02251782092451.2681161951-52.8599620525-26.57454841890.401760336274
94.37342455465-0.540340356235-0.02920873609174.16300530185-5.055682010636.4198764738-0.351919620164-0.5118879834750.791440894458-0.5195722523290.7127236337240.03565221429230.619896239455-0.480636077355-0.3501948502260.958388437645-0.214410276635-0.06741118926631.02596903591-0.2587693124881.28209458668-46.3716457158-22.77276897893.25173762269
102.752526517721.118762641160.1739204741534.570156364070.3275552072291.279646463340.206340777971-0.4089768158740.03710785429440.729420422144-0.3415811418770.209323883563-0.2364231034170.193674435592-0.06599815478380.8617282226150.0343034235779-0.05204051488040.668039934070.01301357883460.833590301938-20.0436695641-39.78021895671.59637352575
113.49268853587-0.6240323536170.2497712206916.16635794503-0.6577582236062.64163647924-0.007128462761210.1066741455720.102082988838-0.6172150484310.187474273472-0.09240550734540.04853639087490.07012403581520.0004390054436990.947664820696-0.1232266067880.0503762033810.656880562029-0.1534323916850.906789438249-9.38749864609-38.8088475269-16.9041656659
125.263527078062.28318992184-0.3969959225485.27898517315-0.05064348109224.15195805983-0.261689018891-0.3508669745080.0609619802807-0.2677368410680.11426050658-0.09160994235380.3516382918440.1987729771990.224829505070.748530109009-0.022951634897-0.02523458807910.580621497065-0.0773144121440.853382840019-12.8304421525-41.4253382452-15.6856762074
138.48681316574-2.07165299127-4.064348004768.839507082121.856121459622.50260675428-0.526609792572-0.56066206192-0.04088672562991.21264397419-0.212266699904-0.4804024016650.8602562691310.2712130385180.6313825042541.065035523240.111376643707-0.2945239065740.7170907495680.1398786062080.732135067715-14.7220941267-34.63295658786.70127005166
142.490448864761.386996504550.7131648786761.58069619803-0.7171089281861.759517470040.675154986886-2.294184136220.6366937960552.163997527260.583385173159-0.9716210523421.23210057811.94887110322-1.080035604841.70906584095-0.275975179654-0.1568854950611.65760113221-0.3797189200231.21469186348-17.9874474005-41.159825601714.9209156654
153.16142464551-1.38098182243-1.055806183025.16332661558-2.290082037696.00727657936-0.189238824072-0.9906503717960.05409390930250.5732692062-0.2040001381670.198032018388-0.0458436151857-0.1944432648310.2745701925591.02365657622-0.2321170361930.1114843632341.24969597656-0.3107205222060.947171708511-45.0275928856-25.403654242623.1008581036
164.937207891361.06161005918-1.931458767323.7022553055-0.5733543401313.782136892110.06225527216180.3029795083060.6182546147240.0249223481020.213951265320.903924742207-0.591874502157-0.455599970585-0.1971967076080.7711800678950.130980129788-0.08444503167340.6700226503530.03968780684610.890774283743-25.9698007988-5.2146180741-20.2215219661
173.34071308449-0.0564630919486-0.6844641764725.20331971756-0.4151771315296.48344192803-0.6463206305771.601091986960.0976228251448-0.1624848170820.529897208625-0.563657229931-0.778600884163-0.4857495235210.07955159853911.26790907884-0.002012643380390.08546738624481.022743837490.007764309723880.939839981721-11.54607605712.98912847262-37.0753030638
185.357511907051.81427525458-1.593490759712.49800946554-0.4109754018731.4416603827-0.0167624790943-0.1214733653861.14022423123-0.5614168452540.2067071306940.46341021661-0.242822659719-0.264054820088-0.03408119432071.137328942880.108556508835-0.1474491681440.619219351504-0.08531422147620.990416946061-22.28228261821.2545996911-22.2674413186
190.7655544564110.04098449590711.36898907082.991897498420.6648972330222.60412968408-0.5589042307921.07926860395-1.296465488770.69613771211.11686190605-0.996588457139-0.3100673587580.151254736454-0.1401386211692.65157607805-0.166697238841-0.2600335408612.490464043410.1379230290952.75459271829-14.9152745646-12.516371208-80.5996055189
202.29202559830.934343676098-1.031003602380.17448342992-0.204743002782.641782956790.3604911881-0.00522344148974-0.215108513052-0.247457360976-0.0392451506650.179008830447-0.320134180637-1.14859106507-0.7463632759872.22066772282-0.02726411374210.3235509895722.010790803480.223261560742.38874198374-53.724139152-14.3419873969-26.1151354114
210.842627690371-1.402078638371.771277363693.001610368-3.328330141356.57180575755-0.008582332383610.6297439791921.2376548738-1.326931959622.01799423151-0.5649838736620.649810159616-0.805292332359-1.497332329661.11922740972-0.0154772373482-0.06482674345912.17851501685-0.1791186530931.84721208993-67.4725802145-25.96852903715.0565741792
222.43000381517-0.0758856501624-0.01825163782890.00796981635347-0.1893476927062.05254844314-0.625093866453-0.975103145703-0.249106229510.1519764175460.5490830808820.6058133739791.34832184138-3.912657371250.2364561211272.16933002771-0.4581845740750.4138679178242.60998320644-0.5896084819051.48233338097-62.1275559762-26.714957778336.6081733245
232.92396529437-0.573294653062-4.124397502350.1494252205880.733958697636.280454184560.0974295192527-0.9681799194241.370032921040.832015981090.1191367461271.14184707758-0.7926767734350.526873034528-0.09552070175832.03398548971-0.3104494889580.07576368782652.20165998499-0.5888103970681.78616456305-53.254083581-27.883081650442.1522234039
242.014983469780.43590744987-0.6882504898980.882291024485-0.2915920870641.441455849-0.347988691587-0.6485218903880.829659683004-0.2709111490580.305714630251-0.543109415082-0.286155257205-1.888883930650.2804042424171.47624524022-0.107847412740.2006279237972.07745811203-0.2794297046542.01399297717-66.5311791507-23.527638036521.3415371507
250.1169593079690.230151825209-0.09686419648450.0765565754646-0.05031377349740.1157629271660.849513784979-0.3765512097140.708273957125-0.1227019586830.1039754583830.186373793544-1.215760993130.524196109122-0.9258016955252.68934349943-0.677370378223-0.2335735537561.56840470687-0.02401625715791.83059759805-39.8981465276-18.3150743566-43.5752353247
260.379727806663-0.7897679478720.4296538699133.17452097333-4.355012863649.102935679770.29800645586-0.2450452495790.7499151487811.28665768811-2.08387271992-0.6033693144410.2062588573340.7108837056361.310593159912.48330887807-0.4218442287060.06612873680681.6066373899-0.1088812503341.86262044007-14.161041761-15.6734566444-85.6282385883
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 86 )AA2 - 861 - 77
22chain 'A' and (resid 87 through 213 )AA87 - 21378 - 204
33chain 'A' and (resid 214 through 239 )AA214 - 239205 - 230
44chain 'A' and (resid 240 through 294 )AA240 - 294231 - 285
55chain 'B' and (resid 1 through 60 )BB1 - 601 - 51
66chain 'B' and (resid 61 through 86 )BB61 - 8652 - 77
77chain 'B' and (resid 87 through 294 )BB87 - 29478 - 283
88chain 'P' and (resid 1 through 28 )PC1 - 281 - 28
99chain 'P' and (resid 29 through 86 )PC29 - 8629 - 82
1010chain 'P' and (resid 87 through 177 )PC87 - 17783 - 173
1111chain 'P' and (resid 178 through 201 )PC178 - 201174 - 197
1212chain 'P' and (resid 202 through 260 )PC202 - 260198 - 256
1313chain 'P' and (resid 261 through 278 )PC261 - 278257 - 274
1414chain 'P' and (resid 279 through 292 )PC279 - 292275 - 288
1515chain 'Q' and (resid 1 through 87 )QD1 - 871 - 87
1616chain 'Q' and (resid 88 through 170 )QD88 - 17088 - 170
1717chain 'Q' and (resid 171 through 234 )QD171 - 234171 - 229
1818chain 'Q' and (resid 235 through 293 )QD235 - 293230 - 288
1919chain 'G' and (resid 4 through 13 )GE4 - 13
2020chain 'G' and (resid 14 through 42 )GE14 - 42
2121chain 'G' and (resid 43 through 47 )GE43 - 47
2222chain 'G' and (resid 48 through 55 )GE48 - 55
2323chain 'H' and (resid 0 through 4 )HF0 - 4
2424chain 'H' and (resid 5 through 14 )HF5 - 14
2525chain 'H' and (resid 15 through 46 )HF15 - 46
2626chain 'H' and (resid 47 through 50 )HF47 - 50

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