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- PDB-3x2r: Structure of the nonameric bacterial amyloid secretion channel CsgG -

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Basic information

Entry
Database: PDB / ID: 3x2r
TitleStructure of the nonameric bacterial amyloid secretion channel CsgG
ComponentsCsgG
KeywordsMEMBRANE PROTEIN / beta-barrel / outer membrane protein / curli secretion / biofim
Function / homologyCurli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile. / outer membrane-bounded periplasmic space / plasma membrane / Curli production assembly/transport component CsgG / CsgG
Function and homology information
Biological speciesEscherichia coli Xuzhou21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHuang, Y. / Cao, B. / Zhao, Y. / Kou, Y. / Ni, D. / Zhang, X.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the nonameric bacterial amyloid secretion channel
Authors: Cao, B. / Zhao, Y. / Kou, Y. / Ni, D. / Zhang, X.C. / Huang, Y.
History
DepositionDec 29, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

Downloads & links

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Assembly

Deposited unit
D: CsgG
A: CsgG
B: CsgG
C: CsgG
E: CsgG
F: CsgG
G: CsgG
H: CsgG
I: CsgG


Theoretical massNumber of molelcules
Total (without water)275,2569
Polymers275,2569
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37850 Å2
ΔGint-166 kcal/mol
Surface area74230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.877, 176.715, 103.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CsgG


Mass: 30584.035 Da / Num. of mol.: 9 / Fragment: Chymotrypsin digest fragment / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli Xuzhou21 (bacteria) / Strain: CFT073 / Gene: CDCO157_1350, csgG / Plasmid: pQLinkN / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: I1ZTN7, UniProt: A0A0F6C2F5*PLUS

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Tris-HCl(pH8.5), 300mM MgCl2, 14% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 61340 / Num. obs: 61340 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3 Å / % possible all: 86.9

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.071 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 34.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 3048 4.98 %random
Rwork0.2438 ---
obs0.2462 61213 86.76 %-
all-61340 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13042 0 0 0 13042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713223
X-RAY DIFFRACTIONf_angle_d1.30217934
X-RAY DIFFRACTIONf_dihedral_angle_d16.5554711
X-RAY DIFFRACTIONf_chiral_restr0.0832137
X-RAY DIFFRACTIONf_plane_restr0.0062310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-2.94540.44051460.3709260887
2.9454-2.99370.42831310.3443266789
2.9937-3.04530.41051350.3314268988
3.0453-3.10060.37521520.3165266990
3.1006-3.16030.35061190.295267989
3.1603-3.22480.3561290.2748271389
3.2248-3.29490.32691610.2834268090
3.2949-3.37150.3081370.2671267489
3.3715-3.45580.32391330.2607266988
3.4558-3.54920.30161550.2568265689
3.5492-3.65360.30621510.2313268989
3.6536-3.77150.30311270.2371265388
3.7715-3.90620.26871680.2273262487
3.9062-4.06250.2791190.2248266087
4.0625-4.24730.2571450.2159262986
4.2473-4.47110.23151150.1904261885
4.4711-4.7510.22111340.1934260985
4.751-5.11740.24531320.2099262585
5.1174-5.63170.29881440.2464257384
5.6317-6.4450.28511430.2611261584
6.445-8.11360.26741300.2506259183
8.1136-48.07780.30251420.2446257579
Refinement TLS params.Method: refined / Origin x: 206.9173 Å / Origin y: 36.5217 Å / Origin z: 5.7516 Å
111213212223313233
T0.459 Å2-0.0073 Å2-0.001 Å2-0.4245 Å20.0089 Å2--0.5825 Å2
L0.8942 °2-0.1585 °2-0.0289 °2-0.2071 °20.0284 °2--0.1854 °2
S-0.0597 Å °-0.1661 Å °-0.0546 Å °0.0849 Å °0.0176 Å °0.0146 Å °-0.001 Å °-0.0217 Å °0.0464 Å °
Refinement TLS groupSelection details: all

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