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- PDB-7r3w: Crystal structure of the albicidin resistance protein STM3175 fro... -

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Basic information

Entry
Database: PDB / ID: 7r3w
TitleCrystal structure of the albicidin resistance protein STM3175 from Salmonella typhimurium
ComponentsPutative bacterial regulatory helix-turn-helix protein
KeywordsDNA BINDING PROTEIN / transcription regulator / albicidin / resistance / DNA-binding
Function / homology
Function and homology information


cellular response to antibiotic / peptide binding / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
: / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Transcription regulator HTH, AraC- type / Regulatory factor, effector binding domain superfamily / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain ...: / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Transcription regulator HTH, AraC- type / Regulatory factor, effector binding domain superfamily / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
Probable HTH-type transcriptional regulator STM3175
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsDimos, N. / Kosol, S. / Suessmuth, R. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SU 239/18-1 Germany
CitationJournal: Plos Biol. / Year: 2023
Title: Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria.
Authors: Saathoff, M. / Kosol, S. / Semmler, T. / Tedin, K. / Dimos, N. / Kupke, J. / Seidel, M. / Ghazisaeedi, F. / Jonske, M.C. / Wolf, S.A. / Kuropka, B. / Czyszczon, W. / Ghilarov, D. / Gratz, S. ...Authors: Saathoff, M. / Kosol, S. / Semmler, T. / Tedin, K. / Dimos, N. / Kupke, J. / Seidel, M. / Ghazisaeedi, F. / Jonske, M.C. / Wolf, S.A. / Kuropka, B. / Czyszczon, W. / Ghilarov, D. / Gratz, S. / Heddle, J.G. / Loll, B. / Sussmuth, R.D. / Fulde, M.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative bacterial regulatory helix-turn-helix protein
B: Putative bacterial regulatory helix-turn-helix protein
C: Putative bacterial regulatory helix-turn-helix protein
D: Putative bacterial regulatory helix-turn-helix protein


Theoretical massNumber of molelcules
Total (without water)147,3024
Polymers147,3024
Non-polymers00
Water00
1
A: Putative bacterial regulatory helix-turn-helix protein


Theoretical massNumber of molelcules
Total (without water)36,8261
Polymers36,8261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative bacterial regulatory helix-turn-helix protein


Theoretical massNumber of molelcules
Total (without water)36,8261
Polymers36,8261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative bacterial regulatory helix-turn-helix protein


Theoretical massNumber of molelcules
Total (without water)36,8261
Polymers36,8261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative bacterial regulatory helix-turn-helix protein


Theoretical massNumber of molelcules
Total (without water)36,8261
Polymers36,8261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.650, 244.920, 139.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Putative bacterial regulatory helix-turn-helix protein


Mass: 36825.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM3175 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZM00

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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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 24093 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 99.6 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.233 / Net I/σ(I): 8.17
Reflection shellResolution: 3.6→3.82 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 3804 / CC1/2: 0.46 / Rrim(I) all: 1.969 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The search model was computed by the Robetta Server

Resolution: 3.6→22.42 Å / SU ML: 0.6493 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3145 1198 5 %
Rwork0.2679 22761 -
obs0.2702 23959 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.56 Å2
Refinement stepCycle: LAST / Resolution: 3.6→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9288 0 0 0 9288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329590
X-RAY DIFFRACTIONf_angle_d0.684713059
X-RAY DIFFRACTIONf_chiral_restr0.04441355
X-RAY DIFFRACTIONf_plane_restr0.00731716
X-RAY DIFFRACTIONf_dihedral_angle_d5.27441260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.750.44681300.4152454X-RAY DIFFRACTION98.51
3.75-3.920.37761320.3712505X-RAY DIFFRACTION99.74
3.92-4.120.3711310.33092508X-RAY DIFFRACTION99.81
4.12-4.380.38261330.30132523X-RAY DIFFRACTION99.89
4.38-4.720.34751330.27422532X-RAY DIFFRACTION100
4.72-5.180.37161320.29692502X-RAY DIFFRACTION99.58
5.18-5.920.3491340.29352559X-RAY DIFFRACTION99.85
5.92-7.420.29911350.26382558X-RAY DIFFRACTION99.45
7.42-22.420.21251380.18052620X-RAY DIFFRACTION98.43
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)
10.60001672936-0.1412810910350.3387173930450.00988588593896-0.1158231317490.891910491102-0.1105836434030.179761855810.1955611019810.0786365001955-0.01027492031790.0498043156829-0.1783887661180.21824848841-0.07689216675490.3010558509310.2558870584260.01289249547640.564793512826-0.05059392765770.48968980409613.6384548044-51.45111724373.00212581107
20.3339428143290.1775069005820.03130423203870.232853166079-0.1471348622050.777365101184-0.0410549098802-0.195417410356-0.0816283314228-0.2977120261880.0573486729273-0.00229811563911-0.230293656237-0.15575384688-6.75249500947E-61.293977540910.02549912464080.212290843561.11818742240.05418810395031.4307259501549.1620689682-110.588375807-16.6838766253
30.6833885603060.0344173175099-0.1314535292260.009173774406510.05937909934660.225799102045-0.08224440990550.00281417394973-0.1241006892460.227488869550.0506118086651-0.0536795945504-0.06288894543940.04955710170395.48204878348E-61.123175782790.02353936567550.0562853944931.25085187547-0.02379967712171.10439577552.99570861758-67.284996497114.0442262974
40.317209633836-0.165164100025-0.1135514325130.08158637417150.1492799207060.3785892390110.01235329409760.001469057021640.0189636984710.152444565527-0.1472161924110.0487293319843-0.147245415275-0.121873092889-1.49639778132E-51.28636929251-0.01099684094930.1473499191111.12505778647-0.02672822917071.305947863435.5343290103-95.3228546099-10.548752636
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid -5 through 287)AA-5 - 2871 - 285
22(chain 'B' and resid -2 through 287)BB-2 - 2871 - 282
33(chain 'C' and resid -2 through 287)CC-2 - 2871 - 282
44(chain 'D' and resid -4 through 287)DD-4 - 2871 - 287

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