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- PDB-7wze: Structure of Transcriptional regulator from Bacillus subtilis (st... -

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Basic information

Entry
Database: PDB / ID: 7wze
TitleStructure of Transcriptional regulator from Bacillus subtilis (strain 168)
ComponentsUncharacterized HTH-type transcriptional regulator YetL
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / 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
HTH-type transcriptional repressor YetL
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsHong, M. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1F1A1045940 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structure-based molecular characterization of the YetL transcription factor from Bacillus subtilis.
Authors: Park, J. / Kim, J. / Choi, Z. / Hong, M.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Uncharacterized HTH-type transcriptional regulator YetL
A: Uncharacterized HTH-type transcriptional regulator YetL


Theoretical massNumber of molelcules
Total (without water)39,1632
Polymers39,1632
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-75 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.178, 76.545, 88.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYS(chain 'A' and (resid 2 through 13 or (resid 14...AB2 - 392 - 39
12ASNASNVALVAL(chain 'A' and (resid 2 through 13 or (resid 14...AB41 - 4341 - 43
13GLUGLULEULEU(chain 'A' and (resid 2 through 13 or (resid 14...AB45 - 6145 - 61
14LEULEUHISHIS(chain 'A' and (resid 2 through 13 or (resid 14...AB63 - 10563 - 105
15LYSLYSVALVAL(chain 'A' and (resid 2 through 13 or (resid 14...AB112 - 139112 - 139
16GLUGLUASPASP(chain 'A' and (resid 2 through 13 or (resid 14...AB141 - 149141 - 149
17PHEPHELYSLYS(chain 'A' and (resid 2 through 13 or (resid 14...AB151 - 153151 - 153
18LEULEULYSLYS(chain 'A' and (resid 2 through 13 or (resid 14...AB155 - 166155 - 166
21GLUGLULYSLYS(chain 'Y' and (resid 2 through 62 or (resid 63...YA2 - 392 - 39
22ASNASNVALVAL(chain 'Y' and (resid 2 through 62 or (resid 63...YA41 - 4341 - 43
23GLUGLULEULEU(chain 'Y' and (resid 2 through 62 or (resid 63...YA45 - 6145 - 61
24LEULEUHISHIS(chain 'Y' and (resid 2 through 62 or (resid 63...YA63 - 10563 - 105
25LYSLYSVALVAL(chain 'Y' and (resid 2 through 62 or (resid 63...YA112 - 139112 - 139
26GLUGLUASPASP(chain 'Y' and (resid 2 through 62 or (resid 63...YA141 - 149141 - 149
27PHEPHELYSLYS(chain 'Y' and (resid 2 through 62 or (resid 63...YA151 - 153151 - 153
28LEULEULYSLYS(chain 'Y' and (resid 2 through 62 or (resid 63...YA155 - 166155 - 166

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator YetL


Mass: 19581.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yetL, BSU07220 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O31541
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 Na acetate, 0.1 Tris, 9.0, 14% glycerol, 32% PEG 4K

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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: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 9627 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 70.08 Å2 / CC1/2: 1 / Net I/σ(I): 55
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 478 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→32.02 Å / SU ML: 0.3317 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.6048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 471 4.92 %472
Rwork0.2115 9106 --
obs0.2158 9577 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 0 6 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722618
X-RAY DIFFRACTIONf_angle_d0.97093501
X-RAY DIFFRACTIONf_chiral_restr0.0495386
X-RAY DIFFRACTIONf_plane_restr0.0061440
X-RAY DIFFRACTIONf_dihedral_angle_d17.52941583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.030.35941590.25252956X-RAY DIFFRACTION99.65
3.03-3.820.28891530.24643028X-RAY DIFFRACTION99.91
3.82-32.020.2881590.19013122X-RAY DIFFRACTION99.24
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)
17.776587280450.1810652433990.2956800614123.34867010578-2.922166088688.42731161237-0.5109803349820.406801089292-0.00316322187350.006572057614430.348295900041-0.4496864616-1.09650459644-0.543296111746-0.1191255483020.7404981630580.1531360258220.2693532618570.6636463075490.3151942112361.0709936191410.53591491614.6436760003-22.2584869424
26.857698826114.4193065116-0.4870942781166.78274679262-3.918802406474.702905607040.5537064169010.06067016891280.4002199896010.8939102974230.02063261498890.200018751975-0.36257705647-0.0256137656132-0.7008879150710.6103598820870.08331235868370.02091823976590.4583246583520.01464777360160.4989456146117.08910300334-0.169145313081-14.310754879
34.501011548782.934937546512.25596607313.80720612624-1.4509258866.11458676185-0.1340079532640.301842118221-0.60608175556-1.160578069440.686029584827-0.3921421754780.986933789521-0.0116529068836-0.244202369710.7294417749690.004541953169520.05460290257640.4653848162760.05161156336390.7893109936729.0971679194-23.8573411689-9.25653962527
49.190622418842.573805386323.036553212472.542118848710.9207957113531.06035146298-1.919354391811.8390505979-0.56395563683-1.327948660491.1750720579-1.326334114230.08220746658621.496326434620.3011960998480.7248483305940.1333847129390.2409606762510.9710941348-0.4417338967690.4962005667519.2766268946-21.4136376204-9.45270307093
54.876535218735.443902022821.684632889627.75008754484-1.43431492199.541461839960.0741692288878-0.9713172343840.00214798316060.945651136412-0.135685197078-0.7617087843470.1239429169-0.413264219889-0.1006881164050.5604768714970.0281797257262-0.01587710708710.539323898572-0.03533110729040.56889737250311.8924485764-22.28742946080.912918797275
61.995878634496.02267683589-8.44787385446.08233082364-3.032604234342.00018280125-1.32780151534-2.83081173876-2.480450941450.288603161352-1.09884841676-2.140383708922.02328445652.15867651753-2.153400140.9578555875230.291908265850.05852443045420.3969626550660.02153881629110.76189973723413.7203195405-31.3651967117-1.46379945612
76.59852335842.320452370241.035223403434.266583911580.7768521474391.55287080433-0.0634734180581-0.1938346668880.505901000103-0.3372565162810.08125994729311.86102007552-0.329371487914-0.692665493774-0.3318467147110.505766713922-0.021571140672-0.1267644441410.5082119515940.02343708578810.770647843144-1.59831782007-20.1908187292-12.6236606999
87.643614605692.305282647692.051843258693.3596027681-2.609093566636.21244602826-0.6424269281351.309370196490.580985964555-1.809017036480.3023174544650.8025394866410.6474674186910.3827957396980.3860791282510.9164004426590.0795701581967-0.135320368370.663221639576-0.03509919933130.93621202637914.6880286393-4.37489035395-25.0960210127
93.340774316993.683267144351.983492753824.166720515962.405026286449.317384222270.1947358098530.447310429093-0.5966243329572.720380580030.7655488422650.1302060700221.899207473072.45641634537-1.319612969691.050108072250.265592506798-0.07137193694740.937662518891-0.1917318869851.7563635569720.1682603102-11.2414510758-16.4084014217
103.510951582070.540889867194-1.632520570491.5949606191-3.670659505748.300027964831.54064359146-0.4165961406830.5831163983251.98212020082-0.4455540343780.09974655869070.341120407687-0.7590755407911.472446804691.668710746730.0796051390456-0.2735933085160.625050069416-0.5064829540641.75182804575.10929065813-21.6761668597-22.4806395132
117.400660891595.398652533196.468078489555.687908012222.102107605617.238654711920.1160328260550.38842961745-0.6249547238420.612409643240.133303511575-0.6780762476220.8747855990570.342722071787-0.3673037307670.6146457875050.1298122738830.01042645232870.54966619249-0.1296272586120.84191989034115.0730875318-2.23007354179-13.7245511366
124.39491465071.76261752456-3.234148828629.394890729912.40430076194.11857067989-0.6394656424680.94659535008-1.53548951167-1.424386875570.358027305821-2.57487615706-0.147330321721-0.780433510825-0.2995355979910.682942779772-0.0606396013074-0.00839730866470.834698911211-0.245703530330.9933961379814.269984263217.5102146099-9.45189110313
131.20786815729-1.306459046532.080247571162.73435241085-3.14697745494.40820220989-0.8378528011332.29731673857-0.0227130903766-0.3068478714650.2998938470991.30095191855-1.39216791573-0.0872025762611-0.5355679705360.896351214525-0.20011331210.1119064589210.896180798545-0.1784171338760.7648635448699.8741985630629.646366216-12.0922204605
146.860757326660.125597747802-1.068648736685.478170477640.1177556495618.258516171840.365921939809-0.137187889419-0.1453263135580.252207345632-0.09486112941810.152603519323-0.950262771476-0.683005715761-0.05632460539230.5850749661820.06301424825190.07608676111940.747981374694-0.05807693102240.6135644209517.0588464343323.5513044378-3.42577856023
156.160597424450.5322398165791.26857574850.86307860774-0.5365746896982.366494731630.144271651186-0.4751243543460.8582185730540.2250897220020.03988814246350.187755905197-0.00912126275130.824280476130.1743297105830.426630993477-0.09211888976290.08658509966220.6448643149330.120038691370.9941203334224.079461239217.9581921986-13.306107347
162.4239083464-0.2035160123921.349671776396.13130189034-2.949355830095.415177218170.03816349223150.7289782231250.0401313206118-1.637742486570.4344386967960.5137875658540.769307294010.0312580259777-0.347970494920.9817334138940.180029327873-0.1205747817150.669046426093-0.09932916237580.6194152954998.907277845761.28052969601-26.0975109138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Y' and (resid 2 through 23 )
2X-RAY DIFFRACTION2chain 'Y' and (resid 24 through 51 )
3X-RAY DIFFRACTION3chain 'Y' and (resid 52 through 73 )
4X-RAY DIFFRACTION4chain 'Y' and (resid 74 through 84 )
5X-RAY DIFFRACTION5chain 'Y' and (resid 85 through 104 )
6X-RAY DIFFRACTION6chain 'Y' and (resid 105 through 118 )
7X-RAY DIFFRACTION7chain 'Y' and (resid 119 through 138 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 139 through 167 )
9X-RAY DIFFRACTION9chain 'A' and (resid 2 through 9 )
10X-RAY DIFFRACTION10chain 'A' and (resid 10 through 23 )
11X-RAY DIFFRACTION11chain 'A' and (resid 24 through 51 )
12X-RAY DIFFRACTION12chain 'A' and (resid 52 through 66 )
13X-RAY DIFFRACTION13chain 'A' and (resid 67 through 73 )
14X-RAY DIFFRACTION14chain 'A' and (resid 74 through 118 )
15X-RAY DIFFRACTION15chain 'A' and (resid 119 through 138 )
16X-RAY DIFFRACTION16chain 'A' and (resid 139 through 166 )

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