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- PDB-7u5q: Crystal structure of transcriptional regulator, GntR family, from... -

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Basic information

Entry
Database: PDB / ID: 7u5q
TitleCrystal structure of transcriptional regulator, GntR family, from Brucella melitensis
ComponentsTranscriptional regulator, GntR family protein
KeywordsDNA BINDING PROTEIN / SSGCID / Transcriptional regulator / GntR / BMEA_B0792 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Transcriptional regulator, GntR family protein
Similarity search - Component
Biological speciesBrucella melitensis ATCC 23457 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be Published
Title: Crystal structure of transcriptional regulator, GntR family, from Brucella melitensis
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, GntR family protein
B: Transcriptional regulator, GntR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8175
Polymers59,6062
Non-polymers2113
Water543
1
A: Transcriptional regulator, GntR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8692
Polymers29,8031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator, GntR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9483
Polymers29,8031
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.320, 83.350, 116.100
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-IDDetails
d_1ens_1(chain "A" and (resid 43 through 46 or (resid 47...
d_2ens_1(chain "B" and (resid 43 through 49 or resid 51...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRTYRA3 - 9
d_12ens_1GLUALAA11 - 217
d_21ens_1THRTYRC1 - 7
d_22ens_1GLUALAC9 - 215

NCS oper: (Code: givenMatrix: (0.911951624188, -0.310526515472, 0.26817441774), (-0.31056471154, -0.949560127003, -0.0434180279527), (0.268130183097, -0.0436903695773, -0.962391477788)Vector: 9. ...NCS oper: (Code: given
Matrix: (0.911951624188, -0.310526515472, 0.26817441774), (-0.31056471154, -0.949560127003, -0.0434180279527), (0.268130183097, -0.0436903695773, -0.962391477788)
Vector: 9.47798748438, 12.3595582834, -53.5479945633)

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Components

#1: Protein Transcriptional regulator, GntR family protein


Mass: 29803.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis ATCC 23457 (bacteria)
Strain: ATCC 23457 / Gene: BMEA_B0792 / Plasmid: BrmeB.18158.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0RLW1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions / Calibre Morpheus screen condition B10 (10% w/v PEG8000, 20% v/v ethylene glycol, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 100 mM bicine/Trizma ...Details: Molecular Dimensions / Calibre Morpheus screen condition B10 (10% w/v PEG8000, 20% v/v ethylene glycol, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 100 mM bicine/Trizma base, pH 8.5) + 30 mg/mL BrmeB.18158.b.B1.PS02075, tray 321296 b10 drop2, direct cryoprotection, puck: agh1-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 8, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15851 / % possible obs: 99.2 % / Redundancy: 6.115 % / Biso Wilson estimate: 88.875 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.087 / Χ2: 0.9 / Net I/σ(I): 13.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.086.1820.8632.3711700.9190.941100
3.08-3.166.2340.6832.9411260.9130.745100
3.16-3.256.2050.5293.6410950.9410.57799.9
3.25-3.356.1530.3554.9910750.9750.388100
3.35-3.466.1780.2596.4310430.9850.282100
3.46-3.596.1630.2018.019970.9860.21999.9
3.59-3.726.1350.13910.589800.9930.152100
3.72-3.876.1460.11312.319290.9950.123100
3.87-4.056.1330.09214.638890.9960.10199.8
4.05-4.246.10.08116.928680.9970.08999.7
4.24-4.476.1150.0718.668270.9970.07699.6
4.47-4.746.1260.06720.487700.9970.07499.4
4.74-5.076.060.06321.67360.9970.06999.3
5.07-5.486.0920.06521.836870.9960.07198.4
5.48-66.0450.06522.046260.9970.07198.1
6-6.716.0640.06324.025660.9950.06998.3
6.71-7.756.0120.05727.075140.9960.06297.3
7.75-9.495.930.05628.334300.9970.06196.4
9.49-13.425.8120.05629.493410.9960.06195
13.42-505.1980.05126.441820.9980.05684.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RoseTTAfold model

Resolution: 3→46.85 Å / SU ML: 0.3502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1560 9.86 %0
Rwork0.1884 14255 --
obs0.1929 15815 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.37 Å2
Refinement stepCycle: LAST / Resolution: 3→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 3 3 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443361
X-RAY DIFFRACTIONf_angle_d0.66394583
X-RAY DIFFRACTIONf_chiral_restr0.0435534
X-RAY DIFFRACTIONf_plane_restr0.0046607
X-RAY DIFFRACTIONf_dihedral_angle_d13.63431231
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.765904130168 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10.32551460.29481271X-RAY DIFFRACTION99.51
3.1-3.210.35711480.28711282X-RAY DIFFRACTION99.51
3.21-3.340.28591300.27011309X-RAY DIFFRACTION99.86
3.34-3.490.30921330.25921285X-RAY DIFFRACTION99.72
3.49-3.670.26041490.23021257X-RAY DIFFRACTION99.93
3.67-3.90.2361340.19641314X-RAY DIFFRACTION99.72
3.9-4.20.24831500.18361287X-RAY DIFFRACTION99.58
4.2-4.620.20651460.16551298X-RAY DIFFRACTION99.38
4.63-5.290.22991480.17231300X-RAY DIFFRACTION98.97
5.29-6.670.24761100.21021334X-RAY DIFFRACTION98.3
6.67-46.850.19131660.14151318X-RAY DIFFRACTION94.58
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)
16.60942342737-3.96709879886-3.928944613835.55082745518-0.399819596854.31555585065-0.601808606205-0.9790987370170.9809710830870.7794465981250.185041862654-0.63405430624-0.2363615399890.5128696731880.3845240823050.836987919773-0.0319581592643-0.2830233564470.70889459004-0.159744713370.98658325920743.9981707423-2.0363241566-7.91219387895
23.881156460971.513529381-2.782798287454.71848609098-3.722027160956.48150432498-0.1168718084580.0132388950065-0.337040489506-0.0175078044303-0.06065861816530.03809843402240.756609890144-0.2557784430240.09834819964030.886461132997-0.0684721615582-0.01139113730490.670918922917-0.1029973659640.62491154169719.3742439856-8.52008675333-15.4640962269
39.375882914493.54415681223-6.103316226933.43222995309-3.196471715085.822096260111.12204019911-1.109814058650.7216521438230.287889268808-0.2819357568640.831656130049-0.425897692714-0.037164843247-0.7914545056070.922467941315-0.0319458941870.1592490649330.814848604796-0.06400529370750.77092568044524.7996791308-1.30818667517-3.13355991572
47.479203805862.57932917308-2.107123161356.050575479780.7699339583993.30302351777-0.0540900187046-0.6139410029330.7869588848440.769560783947-0.05146638763380.721501003622-0.176602875367-0.3943425683980.1837047334580.9088041216670.1847800714880.04873875105610.82384667496-0.0452096287380.7054880752715.4193671839-0.144472896495-8.89640185935
52.608907449040.221150620377-3.566284710647.485379602610.02784221835344.99335915372-0.1089764506350.00580385393999-0.009193245270550.71552219695-0.408833455341-0.460298833936-0.175910690561.711417014751.11235108010.897808416047-0.086307853742-0.2568791293921.494518379660.06271897252791.2685559882846.69277969286.64310288125-31.0550563222
63.325600752381.30807654263-0.9192897386886.40729507535.37970818427.97670051656-0.7318760504130.6976929069530.3948579004290.5723099229340.7933743152580.1644921840310.5508667269151.60276708638-0.2498671563721.202562646270.07588375740120.001148803661271.730053664190.1136851131711.1581335422246.23887578862.17074353343-42.0179267047
75.206128784751.17607290769-0.6631176371697.69315691970.001616803403416.518187718380.329654072706-0.361036085225-0.2061960528290.669370768182-1.54699028559-1.295469643310.2626553260832.15339272380.8216202533651.379083925090.160578823234-0.3491569354911.898164826790.2384958301951.3249255926454.01362854011.05314921932-30.2283698916
82.35834399045-0.7263243969412.924751979636.06719682504-2.48910322394.01575321317-1.29346367064-0.611147294221-1.65813402052-0.1038915909070.983096198249-0.2992944581422.164939056041.763061981560.1362510157781.234023393120.5639242945150.1284195398161.22587535533-0.004727948442531.0468837867142.5864827336-6.93124144997-37.5403794862
91.83916719811-3.60181882411-1.303088790587.384469663681.688034568374.00669041739-0.143611639702-0.0658871714028-0.698119923236-0.3757970104970.05183000115341.18902338550.0267850546595-0.6319344849970.1443546362140.662303957586-0.155693281862-0.1015379810240.752346041959-0.05340135950610.84325080853920.64364811656.54070462207-28.8740845035
101.086507535040.7669211009990.09023048117263.18720785376-1.593626443185.84834746454-0.211201025774-0.05749223349630.820293552747-0.01271544616490.0842072896438-0.272597259549-0.893975216190.2351685301950.1719325395660.970955608424-0.125784224705-0.1124805003930.734699959241-0.03584710324710.79049384559727.033796082718.7216006272-34.8885006263
110.3639645344750.2481120624480.03969416801512.63054558539-4.791248957069.875911389060.2148223324950.06703946772860.270555893261-0.02081493378020.2074809022410.6312374613450.1664454445820.291204094063-0.216274443591.00691872383-0.064532100468-0.189639617040.970867951160.02062228734520.86096200372532.02949537016.23374617852-42.1498948598
126.92598847408-0.96483925096-3.092335614573.629199674390.006583604504359.78835729429-0.1988107618860.155805151072-0.0416938107098-0.315134571307-0.4423798081810.61756126359-1.28129621225-1.024730484340.4679285561460.921724337827-0.00685452096683-0.1429710378480.74678365336-0.05086032248880.9593538340617.387552352116.8609236017-39.6687774301
136.61437005723-4.04913584018-0.7943501577535.458944817210.5169431986024.23042161970.3129745663111.22111244865-1.13968191218-0.829902675314-0.718340460480.6729074684140.153457262246-0.5802793729510.0986250599281.00037016451-0.131104488979-0.02765672027260.956463005795-0.01281779839140.88352707736723.77915047142.33555579021-41.5903565923
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 41 through 113 )AA41 - 1131 - 73
22chain 'A' and (resid 114 through 191 )AA114 - 19174 - 151
33chain 'A' and (resid 192 through 206 )AA192 - 206152 - 166
44chain 'A' and (resid 207 through 257 )AA207 - 257167 - 217
55chain 'B' and (resid 43 through 57 )BC43 - 571 - 15
66chain 'B' and (resid 58 through 68 )BC58 - 6816 - 26
77chain 'B' and (resid 69 through 92 )BC69 - 9227 - 50
88chain 'B' and (resid 93 through 113 )BC93 - 11351 - 71
99chain 'B' and (resid 114 through 134 )BC114 - 13472 - 92
1010chain 'B' and (resid 135 through 189 )BC135 - 18993 - 147
1111chain 'B' and (resid 190 through 206 )BC190 - 206148 - 164
1212chain 'B' and (resid 207 through 226 )BC207 - 226165 - 184
1313chain 'B' and (resid 227 through 257 )BC227 - 257185 - 215

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