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- PDB-2y2t: E. coli CsgC in reduced form -

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Basic information

Entry
Database: PDB / ID: 2y2t
TitleE. coli CsgC in reduced form
ComponentsCURLI PRODUCTION PROTEIN CSGC
KeywordsCHAPERONE / CELL ADHESION / BIOFILM / REDOX / CXC / OXIDOREDUCTASE / IMMUNOGLOBULIN
Function / homologyImmunoglobulin-like - #2420 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesESCHERICHIA COLI O157\:H7 STR. EC4115 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTaylor, J.D. / Salgado, P.S. / Cota, E. / Matthews, S.J.
CitationJournal: Structure / Year: 2011
Title: Atomic Resolution Insights Into Curli Fiber Biogenesis.
Authors: Taylor, J.D. / Zhou, Y. / Salgado, P.S. / Patwardhan, A. / Mcguffie, M. / Pape, T. / Grabe, G. / Ashman, E. / Constable, S.C. / Simpson, P.J. / Lee, W.C. / Cota, E. / Chapman, M.R. / Matthews, S.J.
History
DepositionDec 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Source and taxonomy
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CURLI PRODUCTION PROTEIN CSGC


Theoretical massNumber of molelcules
Total (without water)12,2131
Polymers12,2131
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.972, 80.549, 70.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CURLI PRODUCTION PROTEIN CSGC / CSGC


Mass: 12212.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI O157\:H7 STR. EC4115 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5YVR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINUS CORRESPONDS TO THAT OF THE MATURE PROTEIN.

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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: 2.2 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 25% (W/V) PEG 4000, 30% (V/V) ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 4927 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 4.3 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.946 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27281 226 4.6 %RANDOM
Rwork0.23681 ---
obs0.2385 4643 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 0 19 748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022739
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.9781006
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.094594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61226.55229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79215136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.265153
X-RAY DIFFRACTIONr_chiral_restr0.1280.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.628 9 -
Rwork0.369 333 -
obs--96.88 %
Refinement TLS params.Method: refined / Origin x: 5.9851 Å / Origin y: 12.9402 Å / Origin z: 0.22 Å
111213212223313233
T0.0642 Å2-0.0099 Å2-0.0194 Å2-0.0336 Å20.0097 Å2--0.0217 Å2
L0.9583 °2-0.2873 °2-0.6608 °2-0.9638 °20.2825 °2--2.0851 °2
S-0.0121 Å °-0.0864 Å °-0.0513 Å °-0.2189 Å °0.0099 Å °0.0928 Å °0.0376 Å °0.0233 Å °0.0022 Å °

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