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- PDB-4ncd: Crystal Structure of Class 5 Fimbriae Chaperone CfaA -

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Basic information

Entry
Database: PDB / ID: 4ncd
TitleCrystal Structure of Class 5 Fimbriae Chaperone CfaA
ComponentsGram-negative pili assembly chaperone, N-terminal domain protein
KeywordsCHAPERONE / immunoglobulin fold
Function / homologyImmunoglobulin-like - #3970 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.037 Å
AuthorsBao, R. / Xia, D.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structure of CfaA Suggests a New Family of Chaperones Essential for Assembly of Class 5 Fimbriae.
Authors: Bao, R. / Fordyce, A. / Chen, Y.X. / McVeigh, A. / Savarino, S.J. / Xia, D.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gram-negative pili assembly chaperone, N-terminal domain protein


Theoretical massNumber of molelcules
Total (without water)28,3301
Polymers28,3301
Non-polymers00
Water2,162120
1
A: Gram-negative pili assembly chaperone, N-terminal domain protein

A: Gram-negative pili assembly chaperone, N-terminal domain protein


Theoretical massNumber of molelcules
Total (without water)56,6592
Polymers56,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.606, 28.582, 90.716
Angle α, β, γ (deg.)90.00, 118.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gram-negative pili assembly chaperone, N-terminal domain protein


Mass: 28329.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECP03018675_4907 / Production host: Escherichia coli (E. coli) / References: UniProt: N4NNE0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.3
Details: 22% PEG3350, 0.2 M NaCl, 0.1 M MES pH 5.3, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.54178 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2010
RadiationMonochromator: APS BM22 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 15399 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1
Reflection shellResolution: 2.03→2.08 Å / % possible all: 72.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.037→39.715 Å / SU ML: 0.27 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 2797 10.03 %RANDOM
Rwork0.2174 ---
all0.2213 28845 --
obs0.2213 27884 96.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.037→39.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 0 120 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121735
X-RAY DIFFRACTIONf_angle_d1.3642345
X-RAY DIFFRACTIONf_dihedral_angle_d18.125666
X-RAY DIFFRACTIONf_chiral_restr0.095267
X-RAY DIFFRACTIONf_plane_restr0.007297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.037-2.10980.35642430.31812266X-RAY DIFFRACTION88
2.1098-2.19420.32622800.26112491X-RAY DIFFRACTION94
2.1942-2.29410.40532710.32812440X-RAY DIFFRACTION96
2.2941-2.4150.26732860.24782538X-RAY DIFFRACTION97
2.415-2.56630.23932930.2132584X-RAY DIFFRACTION99
2.5663-2.76440.31052780.21162514X-RAY DIFFRACTION98
2.7644-3.04250.25672890.21742587X-RAY DIFFRACTION99
3.0425-3.48260.22822810.20292578X-RAY DIFFRACTION99
3.4826-4.38680.21742870.18962543X-RAY DIFFRACTION98
4.3868-39.72220.23742890.20162546X-RAY DIFFRACTION97

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