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- PDB-3f84: Structure of fusion complex of major pilin CfaB and major pilin C... -

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Basic information

Entry
Database: PDB / ID: 3f84
TitleStructure of fusion complex of major pilin CfaB and major pilin CfaB of CFA/I pilus from ETEC E. coli
ComponentsCFA/I fimbrial subunit B
KeywordsCELL ADHESION / ETEC / CFA/I / fimbriae / pilus / E. coli / diarrhea / CfaBB / Cell projection / Fimbrium
Function / homologyCFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / CFA/I fimbrial subunit B / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsXia, D. / Li, Y.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.
Authors: Li, Y.F. / Poole, S. / Nishio, K. / Jang, K. / Rasulova, F. / McVeigh, A. / Savarino, S.J. / Xia, D. / Bullitt, E.
History
DepositionNov 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CFA/I fimbrial subunit B
B: CFA/I fimbrial subunit B


Theoretical massNumber of molelcules
Total (without water)64,9052
Polymers64,9052
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-8 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.151, 134.217, 65.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUALAALA2AA4 - 194 - 19
211LEULEUALAALA2BB4 - 194 - 19
121GLUGLUASPASP2AA28 - 4028 - 40
221GLUGLUASPASP2BB28 - 4028 - 40
131LYSLYSASPASP2AA44 - 5144 - 51
231LYSLYSASPASP2BB44 - 5144 - 51
141GLNGLNGLYGLY2AA54 - 9454 - 94
241GLNGLNGLYGLY2BB54 - 9454 - 94
151GLYGLYSERSER2AA97 - 9997 - 99
251GLYGLYSERSER2BB97 - 9997 - 99
161LEULEUALAALA2AA104 - 109104 - 109
261LEULEUALAALA2BB104 - 109104 - 109
171GLYGLYTHRTHR2AA120 - 131120 - 131
271GLYGLYTHRTHR2BB120 - 131120 - 131
181GLNGLNVALVAL2AA138 - 149138 - 149
281GLNGLNVALVAL2BB138 - 149138 - 149
112PROPROSERSER3AA151 - 172151 - 172
212PROPROSERSER3BB151 - 172151 - 172
122THRTHRTHRTHR3AA177 - 189177 - 189
222THRTHRTHRTHR3BB177 - 189177 - 189
132ASPASPASPASP3AA191 - 208191 - 208
232ASPASPASPASP3BB191 - 208191 - 208
142GLNGLNALAALA3AA215 - 236215 - 236
242GLNGLNALAALA3BB215 - 236215 - 236
152LEULEUALAALA3AA239 - 260239 - 260
252LEULEUALAALA3BB239 - 260239 - 260
162SERSERTHRTHR3AA274 - 282274 - 282
262SERSERTHRTHR3BB274 - 282274 - 282
172LYSLYSVALVAL3AA288 - 300288 - 300
272LYSLYSVALVAL3BB288 - 300288 - 300

NCS ensembles :
ID
1
2

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Components

#1: Protein CFA/I fimbrial subunit B / CFA/I pilin / Colonization factor antigen I subunit B / CFA/I antigen


Mass: 32452.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: fusion complex of two CFA/I fimbrial subunits B / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cfaB / Production host: Escherichia coli (E. coli) / References: UniProt: P02971, UniProt: E3PPC4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growMethod: vapor diffusion
Details: The protein, 10 mg/ml in a buffer containing 20 mM Tris-HCl (pH 7.5) and 200 mM NaCl, was mixed in a 1:1 ratio with a well solution containing 30% PEG 8000 and 200 mM ammonium sulfate. VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 32280 / Redundancy: 5.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.874 / SU B: 9.742 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29392 577 2.1 %RANDOM
Rwork0.24247 ---
obs0.24356 27000 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.834 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å20 Å2
2---0.54 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 174 4572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.966096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.27410607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60827.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.163154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023234
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1510.21647
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2640.22939
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.53031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77524906
X-RAY DIFFRACTIONr_scbond_it3.02731430
X-RAY DIFFRACTIONr_scangle_it4.784.51190
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1444tight positional0.140.05
2476tight positional0.130.05
1360medium positional0.350.5
2397loose positional0.395
1444tight thermal0.40.5
2476tight thermal0.480.5
1360medium thermal1.372
2397loose thermal2.5210
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 49
Rwork0.254 1767
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)
12.63861.5602-0.37154.54-1.0316.09880.00480.24380.1154-0.3180.22490.02630.54860.3285-0.22970.04820.0637-0.07620.1781-0.04260.156315.125860.1326-23.9121
21.6843-0.48080.56774.2428-1.72116.0754-0.06210.0059-0.0217-0.12570.08150.2264-0.7393-0.1085-0.01940.1573-0.0281-0.03240.17990.0050.23971.79426.312510.2022
32.1877-1.63911.15347.6173-3.92332.5947-0.0979-0.2064-0.5570.23320.0561-0.0111-0.07970.18080.04180.611-0.0113-0.10410.3695-0.00590.44613.20630.669539.1488
43.17191.6352-1.50193.3549-1.91334.9985-0.0270.07110.0204-0.07770.159-0.04870.0682-0.0861-0.1320.0971-0.0014-0.01090.1791-0.0450.211812.770166.94354.2736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1511 - 151
2X-RAY DIFFRACTION2AA152 - 301152 - 301
3X-RAY DIFFRACTION3BB1 - 1511 - 151
4X-RAY DIFFRACTION4BB152 - 302152 - 302

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