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- PDB-2y2y: Oxidised form of E. coli CsgC -

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Basic information

Entry
Database: PDB / ID: 2y2y
TitleOxidised form of E. coli CsgC
ComponentsCURLI PRODUCTION PROTEIN CSGC
KeywordsCHAPERONE / CXC / OXIDOREDUCTASE / CELL ADHESION / BIOFILM / IMMUNOGLOBULIN
Function / homologyImmunoglobulin-like - #2420 / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / :
Function and homology information
Biological speciesESCHERICHIA COLI O157\:H7 STR. EC4115 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTaylor, J.D. / Salgado, P.S. / Constable, S.C. / Cota, E. / Mathews, 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 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CURLI PRODUCTION PROTEIN CSGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3313
Polymers12,2131
Non-polymers1182
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.490, 36.430, 39.520
Angle α, β, γ (deg.)90.00, 117.45, 90.00
Int Tables number5
Space group name H-MC121

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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
Details: DISULFIDE BOND BETWEEN CYS 29 AND CYS 31
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG 3350, 0.2 M AMMONIUM NITRATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1271
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.99→33.8 Å / Num. obs: 6779 / % possible obs: 95.9 % / Observed criterion σ(I): 4.5 / Redundancy: 3.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.6 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XSK

2xsk


Resolution: 2→21.62 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.876 / SU B: 13.437 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32842 339 5 %RANDOM
Rwork0.26125 ---
obs0.2647 6440 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.458 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→21.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms729 0 8 9 746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.9831014
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.858594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73126.55229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54115136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.479153
X-RAY DIFFRACTIONr_chiral_restr0.1370.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021542
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: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 22 -
Rwork0.213 427 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.4153 Å / Origin y: 10.6001 Å / Origin z: 0.1194 Å
111213212223313233
T0.0442 Å2-0.0042 Å20.0103 Å2-0.0214 Å20.0057 Å2--0.0496 Å2
L2.177 °20.1333 °21.6487 °2-0.72 °20.262 °2--3.4823 °2
S0.0828 Å °-0.1505 Å °-0.0638 Å °0.0211 Å °0.0343 Å °-0.1137 Å °0.0257 Å °-0.2273 Å °-0.1172 Å °

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