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- PDB-5yq0: Crystal structure of secreted protein CofJ from ETEC. -

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Basic information

Entry
Database: PDB / ID: 5yq0
TitleCrystal structure of secreted protein CofJ from ETEC.
ComponentsCofJ
KeywordsCELL ADHESION / Colonization factor / Type IVb pili / CFA/III
Function / homology: / CofJ protein / metal ion binding / CofJ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsOki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. ...Oki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. / Iida, T. / Yoshida, T. / Ohkubo, T. / Nakamura, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization
Authors: Oki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. / Iida, T. / Yoshida, T. / Ohkubo, T. / Nakamura, S.
History
DepositionNov 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CofJ
B: CofJ
C: CofJ
D: CofJ
E: CofJ
F: CofJ
G: CofJ
H: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,49812
Polymers298,3388
Non-polymers1604
Water54,8383044
1
A: CofJ


Theoretical massNumber of molelcules
Total (without water)37,2921
Polymers37,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CofJ


Theoretical massNumber of molelcules
Total (without water)37,2921
Polymers37,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3723
Polymers37,2921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CofJ


Theoretical massNumber of molelcules
Total (without water)37,2921
Polymers37,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3322
Polymers37,2921
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CofJ


Theoretical massNumber of molelcules
Total (without water)37,2921
Polymers37,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: CofJ


Theoretical massNumber of molelcules
Total (without water)37,2921
Polymers37,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: CofJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3322
Polymers37,2921
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.208, 147.540, 149.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid 23 through 47 or resid 51 through 326))
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEASPASPchain AAA23 - 32623 - 326
21ILEILEASPASPchain BBB23 - 32623 - 326
31ILEILEASNASN(chain C and (resid 23 through 47 or resid 51 through 326))CC23 - 4723 - 47
32TYRTYRASPASP(chain C and (resid 23 through 47 or resid 51 through 326))CC51 - 32651 - 326
41ILEILEASPASPchain DDD23 - 32623 - 326
51ILEILEASPASPchain EEE23 - 32623 - 326
61ILEILEASPASPchain FFF23 - 32623 - 326
71ILEILEASPASPchain GGG23 - 32623 - 326
81ILEILEASPASPchain HHH23 - 32623 - 326

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Components

#1: Protein
CofJ


Mass: 37292.191 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cofJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q93I65
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3044 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris-HCl pH 7.0, 14% PEG3350, 200mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.76→49.23 Å / Num. obs: 307221 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.049 / Rrim(I) all: 0.135 / Net I/σ(I): 10.6 / Num. measured all: 2325718 / Scaling rejects: 1340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.797.42.016109819147490.5210.7832.1641.397.6
9.64-49.236.70.0481403320910.9960.020.05228.699.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.2.8data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→49.228 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 30597 9.97 %
Rwork0.1802 276349 -
obs0.1833 306946 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.8 Å2 / Biso mean: 26.7577 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.76→49.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19697 0 4 3044 22745
Biso mean--24.13 35.07 -
Num. residues----2411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820210
X-RAY DIFFRACTIONf_angle_d0.95527346
X-RAY DIFFRACTIONf_chiral_restr0.1052771
X-RAY DIFFRACTIONf_plane_restr0.0063580
X-RAY DIFFRACTIONf_dihedral_angle_d16.0887446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11954X-RAY DIFFRACTION9.163TORSIONAL
12B11954X-RAY DIFFRACTION9.163TORSIONAL
13C11954X-RAY DIFFRACTION9.163TORSIONAL
14D11954X-RAY DIFFRACTION9.163TORSIONAL
15E11954X-RAY DIFFRACTION9.163TORSIONAL
16F11954X-RAY DIFFRACTION9.163TORSIONAL
17G11954X-RAY DIFFRACTION9.163TORSIONAL
18H11954X-RAY DIFFRACTION9.163TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7601-1.78010.367210520.34018749980196
1.7801-1.8010.347610210.305190561007799
1.801-1.8230.323510300.289790691009999
1.823-1.8460.31259750.270391001007599
1.846-1.87030.282510120.254890781009099
1.8703-1.8960.29319860.244891611014799
1.896-1.9230.26479980.234991141011299
1.923-1.95170.257510190.221791091012899
1.9517-1.98220.24689730.211892061017999
1.9822-2.01470.257510340.213290841011899
2.0147-2.04950.24799990.205691581015799
2.0495-2.08680.249310080.206291591016799
2.0868-2.12690.23949970.203292151021299
2.1269-2.17030.242410150.201391791019499
2.1703-2.21750.22519860.1903920310189100
2.2175-2.26910.23049910.183491861017799
2.2691-2.32580.23510610.1892919810259100
2.3258-2.38870.231210710.1908913710208100
2.3887-2.4590.230910600.1858918210242100
2.459-2.53840.22310620.1819922510287100
2.5384-2.62910.211310120.1767926810280100
2.6291-2.73430.219980.1758926910267100
2.7343-2.85880.21310280.1792926010288100
2.8588-3.00950.198210430.1682927810321100
3.0095-3.1980.20359800.1652935210332100
3.198-3.44480.178210250.1576935910384100
3.4448-3.79140.173710100.1451937210382100
3.7914-4.33970.160110300.1384940810438100
4.3397-5.46650.158310060.1404952410530100
5.4665-49.24760.19811150.1899969110806100

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