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- PDB-8yli: Crystal structure of Pectobacterium atrosepticum PecS in complex ... -

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Basic information

Entry
Database: PDB / ID: 8yli
TitleCrystal structure of Pectobacterium atrosepticum PecS in complex with operator DNA
Components
  • (DNA (28-MER)) x 2
  • Regulatory protein
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSong, W.S. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1I1A1A01068105 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
C: DNA (28-MER)
D: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)55,3344
Polymers55,3344
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-92 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 80.504, 75.233
Angle α, β, γ (deg.)90.000, 93.482, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 21 or (resid 22...
d_2ens_1(chain "B" and ((resid 15 through 16 and (name N...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 15 - 175 / Label seq-ID: 6 - 166

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.0108909462793, 0.0539445833372, 0.998484536294), (0.0445790584138, -0.997524753909, 0.0543789747111), (0.998946492481, 0.045103738961, 0.00845918977535)Vector: -2. ...NCS oper: (Code: given
Matrix: (-0.0108909462793, 0.0539445833372, 0.998484536294), (0.0445790584138, -0.997524753909, 0.0543789747111), (0.998946492481, 0.045103738961, 0.00845918977535)
Vector: -2.26947689887, 19.249922158, 1.38368212556)

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Components

#1: Protein Regulatory protein


Mass: 19064.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: pecS, ECA2036 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D5K4
#2: DNA chain DNA (28-MER)


Mass: 8568.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pectobacterium atrosepticum (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8635.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pectobacterium atrosepticum (bacteria)
Has protein modificationN

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium formate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 18873 / % possible obs: 99.2 % / Redundancy: 3 % / CC1/2: 0.992 / Net I/σ(I): 17.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 911 / CC1/2: 0.789 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8YLG

8ylg


Resolution: 2.9→27.46 Å / SU ML: 0.3124 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6395
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2743 1072 5.76 %
Rwork0.2252 17523 -
obs0.2278 18595 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 1142 0 0 3472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633646
X-RAY DIFFRACTIONf_angle_d0.83985193
X-RAY DIFFRACTIONf_chiral_restr0.0422615
X-RAY DIFFRACTIONf_plane_restr0.0067474
X-RAY DIFFRACTIONf_dihedral_angle_d23.92661375
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.339174897283 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.47081300.39212179X-RAY DIFFRACTION98.93
3.03-3.190.34211520.3562122X-RAY DIFFRACTION97.1
3.19-3.390.3671340.26122191X-RAY DIFFRACTION97.81
3.39-3.650.28961680.23812119X-RAY DIFFRACTION97.74
3.65-4.020.25231660.23742196X-RAY DIFFRACTION99.16
4.02-4.60.24361210.20552200X-RAY DIFFRACTION98.35
4.6-5.780.26661100.19632247X-RAY DIFFRACTION99.12
5.79-27.460.1804910.17022269X-RAY DIFFRACTION97.28
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)
11.36768674606-0.657126019871-1.04475296554.583284831521.250630762134.26029535437-0.1643757006960.01848594823260.4640498358670.7043414876910.531612953822-0.308643456405-0.1707335579270.191223431711-0.3552012320960.53898866923-0.009055096559370.1541129731440.342090674763-0.02555526697840.55473032342830.630827460919.095432575926.370693667
23.7843579998-0.338611795123-0.3963160524850.615116163352-0.2345759093047.82139589858-0.175225401095-0.0981014475945-0.270190559744-0.08202991766390.2376007371290.3121687539550.827679797994-0.547597460846-0.1006863465261.11058112889-0.1609233900970.619155820260.3153902789760.06246171214750.60986304844920.648464155-5.9673106241122.507027642
30.3670861647030.484113565644-0.1894236025772.2130029908-2.2386588752.61305250703-0.240333905066-0.0883487239162-0.516437817683-0.4563923190520.31013539276-0.344619748830.63152206206-0.1792262867880.3020995782961.11866732673-0.3231558477070.8202146190970.4198006753880.03554922962711.1277413828112.5077526385-5.9769244507928.857636424
42.48041588643-1.33874880410.9411052862991.30653656311-1.301659870861.53215123565-0.09603757603250.134017319659-0.2444597366390.849337177830.01220032513510.9660159981340.850775910506-0.3922154025150.06478472529130.87650845151-0.1666196474190.3714258824390.549314637348-0.1654495599940.78036512342617.9007060014-8.3060041046521.9378410851
53.06606165593-1.021293566572.161111804363.72504589496-0.531618918534.14521655368-0.123484716761-0.735017633219-0.05472616262391.060816976240.545843831464-0.4772059691890.17085780249-0.140964328361-0.4272044280191.322706580470.009986850762650.03775820240690.348309392794-0.1234183247950.54979705994431.27686123888.2379325025739.1674946805
60.6315256994370.906891773587-0.5399899938671.31385773695-0.7537138187990.676699085755-0.266677331544-0.137159713882-0.1947495496871.634077702590.05013441034040.6310250005390.363588768771-0.3036539951880.1543222370061.496995033450.00933583493050.4557783696130.487405219690.02229008164240.55564643426124.76125785793.1801320391233.0378066539
72.652308011840.01911768841710.03795072064172.301601092721.644095487745.1102381939-0.09386466140120.4086974125150.71737568377-0.3206660402090.130099068265-0.143519861463-1.15247869147-0.148802354946-0.1528860858680.6552956044030.06115248768660.2429245163890.4382056322980.0921042297350.44875309265220.695579548128.832489343113.8685751361
84.45080948345-2.723438767061.031059761966.35090130333-2.031982473313.01782478932-0.271883185091-0.1316482705260.2632478153551.452080155420.253435027635-0.546247544796-0.46831003126-0.3227520452210.014670436130.770703972210.05650407931850.05580296067680.348885697512-0.04034453981960.48707932238327.886781259122.119215551333.2968619752
91.840116764280.296034578610.2608936831850.238717224715-0.196247605853.044417244550.223215986699-0.223059021120.1283791400160.3630442730750.4538038104740.4835173584720.0719955258631-0.879816412855-0.1811369884961.28853585183-0.5701137432111.40597756261.141724616030.3231468368421.78202263486-6.91478062752-2.1236703177631.4222682725
103.624115882211.4313767883-3.059557836762.86761684361-3.253901327835.54820875652-0.2870441175380.707562417224-0.138405853679-1.382647743940.2755771023310.4953351687260.509115925711-0.0287534421140.1639520838671.66261904945-0.127713878310.7586006943720.9517285166190.0427701567290.685926488920.289060478618.25966125942.08952061106
110.2398286174540.304726398282-0.4605721144220.554814211845-1.218003801783.36012124124-0.2893027469450.549711036484-0.227354093672-0.2285327364970.139025815917-0.06902354107550.896270689409-0.2492128157180.4380069360511.6108995934-0.4096125774651.020900119191.179623128490.2511027241291.0350116870834.825831392823.0132906114-12.4629520356
120.391276711429-0.4184043227240.7917985563884.764639519230.2800636369234.03332566616-0.7834304104830.666563787651-0.480534537024-0.6676367921320.5175195980950.7966177634620.853382641428-1.110152787130.272632525730.990877652476-0.1747371496550.4628850305960.8833094511220.05257440095050.9735561954612.946676062613.36943793379.99630877899
131.976284641451.051245606270.1432957994780.714689800833-0.1529557140570.732627206645-0.1767538789640.1077134799330.150085263477-0.260134209970.4175060266580.1162022674730.0284561256903-0.329985674776-0.3433053713431.15287969251-0.4373234490561.01403560521.482375878770.08874583532952.10864068163-8.93745430895-5.2343991317432.8668082022
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 60 )AA15 - 601 - 46
22chain 'A' and (resid 61 through 76 )AA61 - 7647 - 62
33chain 'A' and (resid 77 through 94 )AA77 - 9463 - 80
44chain 'A' and (resid 95 through 152 )AA95 - 15281 - 138
55chain 'A' and (resid 153 through 175 )AA153 - 175139 - 161
66chain 'B' and (resid 14 through 60 )BB14 - 601 - 47
77chain 'B' and (resid 61 through 128 )BB61 - 12848 - 115
88chain 'B' and (resid 129 through 175 )BB129 - 175116 - 162
99chain 'C' and (resid 1 through 10 )CC1 - 10
1010chain 'C' and (resid 11 through 28 )CC11 - 28
1111chain 'D' and (resid 1 through 5 )DD1 - 5
1212chain 'D' and (resid 6 through 20 )DD6 - 20
1313chain 'D' and (resid 21 through 28 )DD21 - 28

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