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- PDB-5xp0: Crystal structure of master biofilm regulator CsgD regulatory domain -

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Basic information

Entry
Database: PDB / ID: 5xp0
TitleCrystal structure of master biofilm regulator CsgD regulatory domain
ComponentsProbable csgAB operon transcriptional regulatory protein
KeywordsTRANSCRIPTION / CsgD / response regulator / signal transduction / phosphorylation
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Probable csgAB operon transcriptional regulatory protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWen, Y. / Ouyang, Z.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain.
Authors: Wen, Y. / Ouyang, Z. / Devreese, B. / He, W. / Shao, Y. / Lu, W. / Zheng, F.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable csgAB operon transcriptional regulatory protein
B: Probable csgAB operon transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9174
Polymers35,8692
Non-polymers492
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-25 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.758, 57.758, 207.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Probable csgAB operon transcriptional regulatory protein / master biofilm regulato


Mass: 17934.318 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: csgD, STM1142 / Production host: Escherichia coli (E. coli) / References: UniProt: O54294
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: (1) 1.6M magnesium sulfate heptahydrate, 0.1M MES, pH 6.5 (2) 1.5M ammonium sulfate, 0.1M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→44.355 Å / Num. obs: 24586 / % possible obs: 99.1 % / Redundancy: 24.4 % / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.355 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.52
RfactorNum. reflection% reflection
Rfree0.2382 2000 8.14 %
Rwork0.2064 --
obs0.209 24580 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→44.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 2 99 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122152
X-RAY DIFFRACTIONf_angle_d1.2862923
X-RAY DIFFRACTIONf_dihedral_angle_d13.8891291
X-RAY DIFFRACTIONf_chiral_restr0.066342
X-RAY DIFFRACTIONf_plane_restr0.008367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.26671390.241572X-RAY DIFFRACTION100
2.05-2.10540.2791400.2231576X-RAY DIFFRACTION100
2.1054-2.16740.21451400.20171586X-RAY DIFFRACTION100
2.1674-2.23740.23531410.19331592X-RAY DIFFRACTION100
2.2374-2.31730.23961420.19561608X-RAY DIFFRACTION100
2.3173-2.41010.24241430.20641605X-RAY DIFFRACTION100
2.4101-2.51980.21261410.19551588X-RAY DIFFRACTION100
2.5198-2.65260.24791420.21911617X-RAY DIFFRACTION100
2.6526-2.81880.26631430.23661610X-RAY DIFFRACTION100
2.8188-3.03640.2411450.24741636X-RAY DIFFRACTION100
3.0364-3.34180.2731440.22721623X-RAY DIFFRACTION100
3.3418-3.82520.22941300.19071468X-RAY DIFFRACTION89
3.8252-4.81840.18961500.17011697X-RAY DIFFRACTION100
4.8184-44.36550.26121600.21281802X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.2499 Å / Origin y: 2.4254 Å / Origin z: -24.5922 Å
111213212223313233
T0.1171 Å20.0241 Å2-0.0081 Å2-0.2708 Å2-0.0029 Å2--0.2301 Å2
L1.1399 °2-0.0105 °2-0.3225 °2-1.785 °20.7505 °2--2.511 °2
S-0.1059 Å °-0.0576 Å °-0.068 Å °0.0175 Å °0.1852 Å °-0.0117 Å °0.1581 Å °0.1473 Å °-0.0606 Å °
Refinement TLS groupSelection details: all

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