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- PDB-4ijy: Crystal Structure of the ETEC Secreted Protein CofJ -

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Basic information

Entry
Database: PDB / ID: 4ijy
TitleCrystal Structure of the ETEC Secreted Protein CofJ
ComponentsCofJ
KeywordsUNKNOWN FUNCTION / Beta-sandwich / SECRETED PROTEIN
Function / homology: / CofJ protein / metal ion binding / IODIDE ION / CofJ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsCraig, L. / Kolappan, S. / Yuen, A.S.W.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structure and secretion of CofJ, a putative colonization factor of enterotoxigenic Escherichia coli.
Authors: Yuen, A.S. / Kolappan, S. / Ng, D. / Craig, L.
History
DepositionDec 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,67613
Polymers37,2921
Non-polymers1,38412
Water1,06359
1
A: CofJ
hetero molecules

A: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35226
Polymers74,5842
Non-polymers2,76724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6490 Å2
ΔGint-14 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.489, 143.489, 59.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-412-

GOL

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Components

#1: Protein CofJ


Mass: 37292.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cofJ / Production host: Vibrio cholerae (bacteria) / References: UniProt: Q93I65
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.72 Å3/Da / Density % sol: 73.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM BisTris (pH 6.5), 200 mM NaI and 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.979
SYNCHROTRONSSRL BL9-220.91
SYNCHROTRONSSRL BL9-230.9794
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDFeb 22, 2008
MARMOSAIC 325 mm CCD2CCDJul 22, 2008
MARMOSAIC 325 mm CCD3CCDJul 22, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
3Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.911
30.97941
ReflectionResolution: 2.6→20 Å / Num. all: 21847 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.783 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24082 1123 5.2 %RANDOM
Rwork0.21229 ---
obs0.21377 20666 100 %-
all-21847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 32 59 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222567
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.943467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57624.565138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47615431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6581514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212004
X-RAY DIFFRACTIONr_mcbond_it0.3261.51510
X-RAY DIFFRACTIONr_mcangle_it0.6522432
X-RAY DIFFRACTIONr_scbond_it1.13331057
X-RAY DIFFRACTIONr_scangle_it1.8754.51035
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 94 -
Rwork0.287 1468 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 53.128 Å / Origin y: -49.4074 Å / Origin z: -24.0103 Å
111213212223313233
T0.0967 Å2-0.0452 Å2-0.0104 Å2-0.0277 Å2-0.0076 Å2--0.0531 Å2
L3.2898 °20.5075 °2-0.2086 °2-1.1887 °2-0.2861 °2--1.9351 °2
S0.0404 Å °-0.0696 Å °-0.0471 Å °-0.0483 Å °-0.0202 Å °0.0695 Å °0.2884 Å °-0.0815 Å °-0.0202 Å °

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