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- PDB-4qs4: Crystal Structure of CofB from Enterotoxigenic Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4qs4
TitleCrystal Structure of CofB from Enterotoxigenic Escherichia coli
ComponentsCofB
KeywordsCELL ADHESION / Type IV pilin fold
Function / homology
Function and homology information


: / : / : / CofB, pilin domain / CofB beta-repeat domain / CofB C-terminal domain / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKolappan, S. / Craig, L.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Minor Pilin CofB, the Initiator of CFA/III Pilus Assembly in Enterotoxigenic Escherichia coli.
Authors: Kolappan, S. / Ng, D. / Yang, G. / Harn, T. / Craig, L.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Nov 27, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: CofB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7806
Polymers54,3111
Non-polymers4685
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CofB
hetero molecules

A: CofB
hetero molecules

A: CofB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,33918
Polymers162,9343
Non-polymers1,40515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area30060 Å2
ΔGint-184 kcal/mol
Surface area61930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.895, 104.895, 362.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

21A-831-

HOH

31A-857-

HOH

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Components

#1: Protein CofB


Mass: 54311.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cofB / Production host: Escherichia coli (E. coli) / References: UniProt: Q93I73
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM MES, 1.65 M Ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL14-111
SYNCHROTRONSSRL BL7-120.97591, 0.979369
SSRL BL7-13
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 22, 2014Mirrors
ADSC QUANTUM 315r2CCDFeb 22, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray2
3Si(111)MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.975911
30.9793691
ReflectionResolution: 2→120.7 Å / Num. all: 52399 / Num. obs: 52381 / % possible obs: 99.96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.093 / Net I/σ(I): 24.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.08-2.1411.20.8513.337261,2100
2.03-2.089.40.9782.538321,2100
2.08-2.1411.20.8513.337261,2100
2.14-2.211.30.6774.136331,2100
2.2-2.2711.30.5465.135321,2100
2.27-2.3511.20.4276.734261,2100
2.35-2.411.30.3547.933151,2100
2.4-2.511.30.3049.232061,2100
2.5-2.611.30.23411.630641,2100
2.6-2.811.30.18814.329731,2100
2.8-2.911.30.14617.928421,2100
2.9-3.111.30.10823.127071,2100
3.1-3.311.30.07631.925481,299.9
3.3-3.511.20.05641.224381,299.9
3.5-3.811.20.04450.922531,299.9
4.2-4.811.20.02876.418971,299.9
4.8-5.7110.02880.216831,299.8
5.7-7.310.90.0369.514341,299.7
7.3-12.610.70.02675.911441,299.5
12.6-120.79.90.018906591,298.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→38.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.744 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22856 2673 5.1 %RANDOM
Rwork0.20521 ---
obs0.2064 52379 99.96 %-
all-52381 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.39 Å20 Å2
2--0.39 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 28 165 3996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023901
X-RAY DIFFRACTIONr_bond_other_d0.0010.023645
X-RAY DIFFRACTIONr_angle_refined_deg1.041.965288
X-RAY DIFFRACTIONr_angle_other_deg0.6723.0028412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76425.723173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5215669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8231516
X-RAY DIFFRACTIONr_chiral_restr0.0620.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 194 -
Rwork0.27 3637 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.29720.4711-1.01791.8368-0.68192.00890.1188-0.02290.49650.0655-0.00180.0947-0.40790.1247-0.1170.142-0.02040.02330.0852-0.00840.0819-12.766-40.996-42.4989
20.62970.0727-0.08110.0552-0.02651.88480.0352-0.0259-0.0111-0.00170.0430.0391-0.0716-0.3129-0.07820.1015-0.00080.01010.10360.03110.057-6.1591-60.1508-5.4715
31.1910.2672-0.60550.9498-0.40623.71950.0131-0.1278-0.02160.2125-0.0395-0.2621-0.07530.42390.02640.0672-0.0253-0.0430.0763-0.02210.093511.9336-59.087937.9229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 256
2X-RAY DIFFRACTION2A257 - 371
3X-RAY DIFFRACTION3A372 - 518

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