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- PDB-7trv: Crystal Structure of the DNA-Binding Domain of the LysR family Tr... -

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Basic information

Entry
Database: PDB / ID: 7trv
TitleCrystal Structure of the DNA-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis
ComponentsLysR-family transcriptional regulatory protein
KeywordsTRANSCRIPTION / LysR transcriptional regulator / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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
FORMIC ACID / Regulator
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKim, Y. / Tesar, C. / Crawford, M. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the DNA-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis
Authors: Kim, Y. / Tesar, C. / Crawford, M. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR-family transcriptional regulatory protein
B: LysR-family transcriptional regulatory protein
C: LysR-family transcriptional regulatory protein
D: LysR-family transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,74024
Polymers41,4664
Non-polymers1,27420
Water3,549197
1
A: LysR-family transcriptional regulatory protein
B: LysR-family transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,39712
Polymers20,7332
Non-polymers66410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-99 kcal/mol
Surface area9690 Å2
MethodPISA
2
C: LysR-family transcriptional regulatory protein
D: LysR-family transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,34312
Polymers20,7332
Non-polymers61010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-92 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.943, 146.270, 33.701
Angle α, β, γ (deg.)90.000, 90.205, 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

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
LysR-family transcriptional regulatory protein / Putative regulator


Mass: 10366.495 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: lysR10, y2171, YP_1951 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8D0G2

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Non-polymers , 5 types, 217 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.025 M Magnesium sulfate, 0.05 M TRIS HCl pH 8.5, 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27328 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.071 / Rrim(I) all: 0.158 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.957 / Num. unique obs: 1352 / CC1/2: 0.599 / Rpim(I) all: 0.552 / Rrim(I) all: 1.111 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→32.84 Å / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 26.6024
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 1428 5.31 %
Rwork0.1873 25747 -
obs0.1957 27192 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 65 197 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022961
X-RAY DIFFRACTIONf_angle_d0.38263982
X-RAY DIFFRACTIONf_chiral_restr0.0317435
X-RAY DIFFRACTIONf_plane_restr0.003512
X-RAY DIFFRACTIONf_dihedral_angle_d12.26451114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.33881210.30752382X-RAY DIFFRACTION86.56
1.86-1.940.32771420.27122609X-RAY DIFFRACTION94.26
1.94-2.030.26951360.24922562X-RAY DIFFRACTION93.57
2.03-2.130.27911510.24752579X-RAY DIFFRACTION93.61
2.13-2.270.25221290.23242626X-RAY DIFFRACTION94.7
2.27-2.440.25911240.21072611X-RAY DIFFRACTION94.84
2.44-2.690.2831510.21162592X-RAY DIFFRACTION93.44
2.69-3.080.24491610.19872612X-RAY DIFFRACTION93.75
3.08-3.880.20021450.16162595X-RAY DIFFRACTION94.23
3.88-32.840.2181670.15122597X-RAY DIFFRACTION93.22
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)
10.3026268822440.3140145147930.2383844875861.260824648470.05553355398992.12107191948-0.0415856954923-0.01060518725430.185339009256-0.0882569531486-0.0126190155084-0.0383841342823-0.0844212882328-0.09209085059240.02792206345720.1818147740020.003544069842270.0314630308190.1512468185390.01143737337420.6946133639923.4627922820312.985917395310.9660352024
22.17660223916-1.948488260211.145688671345.07271195669-2.430469993052.02989235574-0.118991205388-0.01857587980.4301532208230.374363053859-0.119944954712-0.364617425018-0.1011165769940.02692904104480.3094773663740.256037658291-0.01816999186970.03892852492780.163444453333-0.03442587942520.5647828763971.783209388883.7908843655922.0452627409
30.7806729288930.545342067018-0.1823631468371.807736966210.1646593586140.989370518943-0.04858975162050.1577517306240.18700050672-0.0959238098518-0.07531702558560.09726618175050.0379821151647-0.03287863293120.1357102333360.2125969418120.01948121684560.007555723185660.1845708804990.02701885544690.57242702865511.7331298233-10.189293821411.7417014599
41.99370492433-0.2235525305130.6135047529450.577326249308-0.3448634894620.892728163378-0.0362067205821-0.0644656227092-0.103160297756-0.0009304564460630.0210940880502-0.04478046413840.0853468254913-0.0340285555301-0.01127919807790.161773033449-0.02073293258750.004599962675030.1573789009340.04042745849060.7435934729434.17018205115-9.2555473637218.6804819547
53.644983668310.243391098626-0.3693580211370.499933550577-0.4251630259683.594251958170.0839943844259-0.052166071468-0.00329784795452-0.109168219262-0.0141027200418-0.1862489671970.2287585788260.147556675891-0.04876746679990.239021261282-0.006788847472070.002232078532420.124974436662-0.02943657919740.31592283800311.889115851124.2826165837-5.80158684738
62.34137490906-2.49197386841-1.178542689314.818468179091.921865109351.81203755625-0.172320423325-0.363609163215-0.5335473857970.449176021511-0.04815215189040.3501102114740.2010552354790.03520593462810.2046144633640.233256161941-0.03165932828810.001119066934470.2170349217750.0111744827480.52657242288313.027048519733.85692380725.34572117311
73.58488838011.098824364870.8563624592124.382079515721.496570625722.022528344430.1122963315140.0338841026864-0.250928410307-0.110509930498-0.231987938115-0.1081082231180.0562676962580.06301548471780.07953809358650.138712398310.009387266174730.01845204841550.189714970922-0.02317921862540.5120365838096.5130143570243.6017144734-1.73550620173
80.687893604441.735129506480.9253216015135.496757097411.351780680562.1311902085-0.03087277213060.271296719110.0164602736468-0.3442474553570.305211630994-0.2172466865960.04579420443640.119058623983-0.193650984270.278365182685-0.04021863323680.05599814428410.293055805099-0.000995277960490.5904557659596.6209373953452.6996523543-11.0175490271
90.489782851106-0.0108375110113-0.01202691520043.49214178887-1.911035904621.47422936413-0.05126770997790.03754773094850.259594634362-0.2108284394570.01461559317910.07841849636320.0957949574283-0.02489872824280.006088176185910.200381356990.000920872796381-0.07737661765980.167272774906-0.02897986215640.763235630656-2.4555825725746.2849104049-3.77407153002
107.738967934261.76180603784-1.368546743430.921034391761.155674475554.383112382820.2012826423750.2581929998710.852721782963-0.281298335047-0.195951498703-0.224305797332-0.775299016928-0.129758925311-0.07248097770740.318661483237-0.002013477733480.04047878736960.197923434156-0.0177428517040.424127258861-0.26889670966458.05711276763.00160981174
114.46392746024-1.30460932257-1.631128625461.226859065980.7115181297281.222994744540.253080918968-0.1667830523220.270766062844-0.1011294817870.0194151457301-0.464217918568-0.1564669165540.116574868565-0.1522560359940.232027444623-0.0198674959401-0.0006541306577560.163456263162-0.02560127974480.35488073351616.09117271742.47848872790.964733155493
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 59 )AA-2 - 591 - 62
22chain 'A' and (resid 60 through 86 )AA60 - 8663 - 89
33chain 'B' and (resid 0 through 44 )BD0 - 441 - 45
44chain 'B' and (resid 45 through 87 )BD45 - 8746 - 86
55chain 'C' and (resid -2 through 59 )CJ-2 - 591 - 62
66chain 'C' and (resid 60 through 86 )CJ60 - 8663 - 89
77chain 'D' and (resid -1 through 16 )DM-1 - 161 - 18
88chain 'D' and (resid 17 through 29 )DM17 - 2919 - 31
99chain 'D' and (resid 30 through 44 )DM30 - 4432 - 46
1010chain 'D' and (resid 45 through 59 )DM45 - 5947 - 61
1111chain 'D' and (resid 60 through 87 )DM60 - 8762 - 89

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