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- PDB-4q79: Structure of a HG-derivative CsgG -

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Basic information

Entry
Database: PDB / ID: 4q79
TitleStructure of a HG-derivative CsgG
ComponentsCsgG
KeywordsMEMBRANE PROTEIN / beta barrel / alpha-helix / curli secretion / out membrane
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: 3.1 Å
AuthorsHuang, Y. / Zhang, C.X. / Cao, B. / Zhao, Y. / Kou, Y. / Ni, D.
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
DepositionApr 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,06218
Polymers275,2569
Non-polymers1,8059
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39010 Å2
ΔGint-356 kcal/mol
Surface area73840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.640, 176.880, 104.990
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli Xuzhou21 (bacteria) / Gene: CDCO157_1350 / Production host: Escherichia coli (E. coli) / References: UniProt: I1ZTN7, UniProt: A0A0F6C2F5*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50mM Tris-HCl (pH 8.5), 300mM MgCl2, 14% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.006 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: 1.006 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 66194 / % possible obs: 60 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→50 Å / % possible all: 59.2

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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: 3.1→49.247 Å / SU ML: 0.44 / σ(F): 0.9 / Phase error: 42.42 / Stereochemistry target values: MLHL
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 3337 5.04 %random
Rwork0.236 ---
all0.24 66194 --
obs0.2381 66194 58.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13026 0 9 0 13035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613198
X-RAY DIFFRACTIONf_angle_d1.20717905
X-RAY DIFFRACTIONf_dihedral_angle_d17.0794690
X-RAY DIFFRACTIONf_chiral_restr0.082137
X-RAY DIFFRACTIONf_plane_restr0.0052306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0859-3.130.4775690.445116627
3.13-3.17670.4721740.434136430
3.1767-3.22630.4528690.4331141231
3.2263-3.27920.5214830.4093152634
3.2792-3.33570.4118770.3437159136
3.3357-3.39640.4998970.3215171138
3.3964-3.46170.43171030.3021176039
3.4617-3.53230.3311890.2834189642
3.5323-3.60910.3362980.2712198444
3.6091-3.6930.3176950.2641205446
3.693-3.78540.28661120.2583216348
3.7854-3.88770.34961380.2392230151
3.8877-4.0020.25531260.2238239254
4.002-4.13110.29631300.2185250056
4.1311-4.27870.27291380.206272260
4.2787-4.44990.21891470.1679289664
4.4499-4.65230.26861830.1824304468
4.6523-4.89730.23091600.198330873
4.8973-5.20390.27882010.2081356180
5.2039-5.60510.28162090.2502389887
5.6051-6.16830.32012320.2437433297
6.1683-7.05860.27242450.23464489100
7.0586-8.88450.2262440.21714469100
8.8845-49.25310.25392180.252431896

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