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- PDB-2ynk: Wzi, an Outer Membrane Protein Involved in Group 1 Capsule Assemb... -

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Basic information

Entry
Database: PDB / ID: 2ynk
TitleWzi, an Outer Membrane Protein Involved in Group 1 Capsule Assembly in Escherichia coli, is a Carbohydrate Binding Beta-Barrel
ComponentsWZI
KeywordsMEMBRANE PROTEIN / CAPSULE EXPORT
Function / homology
Function and homology information


Capsule assembly protein Wzi / Capsule assembly protein Wzi / Capsule assembly protein Wzi superfamily / Capsule assembly protein Wzi / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DODECANE / HEXANE / N-OCTANE / Capsule assembly Wzi family protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsBushell, S.R. / Mainprize, I.L. / Wear, M.A. / Lou, H. / Kong, L. / Davis, B. / Bayley, H. / Whitfield, C. / Naismith, J.H.
CitationJournal: Structure / Year: 2013
Title: Wzi is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia Coli.
Authors: Bushell, S.R. / Mainprize, I.L. / Wear, M.A. / Lou, H. / Whitfield, C. / Naismith, J.H.
History
DepositionOct 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WZI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39819
Polymers51,0901
Non-polymers2,30918
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.660, 152.080, 95.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein WZI


Mass: 51089.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: B44 / References: UniProt: Q8GNN6
#2: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18
#3: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H26
#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.66 Å3/Da / Density % sol: 73.61 % / Description: NONE
Crystal growDetails: SEE PAPER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97862
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 31, 2010 / Details: TOROIDAL FOCUSSING MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.64→59.37 Å / Num. obs: 28226 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 2.64→2.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.64→59.37 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.887 / SU B: 23.784 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27905 1483 5.1 %RANDOM
Rwork0.24481 ---
obs0.24656 27740 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.64→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 162 14 3652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023722
X-RAY DIFFRACTIONr_bond_other_d0.0010.022652
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9494989
X-RAY DIFFRACTIONr_angle_other_deg0.75836423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3724.317183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81515515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8781520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
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: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 92 -
Rwork0.397 1883 -
obs--98.65 %
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)
10.6318-0.1793-0.33620.8650.03171.7917-0.001-0.03180.1410.01240.08580.1345-0.0291-0.2481-0.08490.0189-0.02730.01120.11540.01840.2102108.59171.01924.272
20.5725-0.31960.02240.8396-0.09351.13-0.00030.1292-0.0292-0.10970.08640.07560.161-0.1491-0.08620.0461-0.0682-0.01320.1518-0.00470.1866112.6559.70213.36
37.3016-1.9747-2.31110.60881.25246.5168-0.07880.519-0.1340.0326-0.15360.0850.4127-0.33690.23250.225-0.042-0.00920.24280.00150.3206129.1757.0913.829
47.84910.8662-5.00361.0467-0.9194.9438-0.30650.0543-0.7004-0.00260.00110.04120.5115-0.27170.30540.2024-0.07310.00870.08780.00280.2143110.94649.33226.837
522.30716.444114.105217.408512.57939.86270.21420.2288-0.83670.2466-0.21550.6690.2940.02290.00130.57040.0570.0840.34770.07250.474125.37343.85214.449
65.7037-1.7285-2.43351.95881.1963.5558-0.0373-0.4022-0.3021-0.06270.03890.1220.31560.0954-0.00170.1585-0.077200.10.05050.1745116.11253.40532.987
71.04440.0815-0.71050.51070.32252.4157-0.0246-0.2160.01560.03260.077-0.06680.1170.1175-0.05250.018-0.0184-0.00360.1232-0.0130.1908123.47965.19832.901
85.9251-2.95493.26743.1464-1.39565.67830.0071-0.25010.30580.0604-0.0332-0.00820.0828-0.32010.02610.0263-0.03230.03790.0577-0.04020.2344117.25679.44132.759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 153
2X-RAY DIFFRACTION2A154 - 254
3X-RAY DIFFRACTION3A255 - 274
4X-RAY DIFFRACTION4A286 - 316
5X-RAY DIFFRACTION5A317 - 322
6X-RAY DIFFRACTION6A323 - 359
7X-RAY DIFFRACTION7A360 - 459
8X-RAY DIFFRACTION8A460 - 477

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