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- PDB-2w8i: Crystal structure of Wza24-345. -

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Basic information

Entry
Database: PDB / ID: 2w8i
TitleCrystal structure of Wza24-345.
ComponentsPUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN
Function / homology
Function and homology information


polysaccharide transmembrane transporter activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
wza like fold / wza like domain / : / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain / Soluble ligand binding domain ...wza like fold / wza like domain / : / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain / Soluble ligand binding domain / SLBB domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative outer membrane lipoprotein Wza
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHagelueken, G. / Ingledew, W.J. / Huang, H. / Petrovic-Stojanovska, B. / Whitfield, C. / ElMkami, H. / Schiemann, O. / Naismith, J.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Peldor Distance Fingerprinting of the Octameric Outer-Membrane Protein Wza from Escherichia Coli.
Authors: Hagelueken, G. / Ingledew, W.J. / Huang, H. / Petrovic-Stojanovska, B. / Whitfield, C. / Elmkami, H. / Schiemann, O. / Naismith, J.H.
History
DepositionJan 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
B: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
C: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
D: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
E: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
F: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
G: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA
H: PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA


Theoretical massNumber of molelcules
Total (without water)287,1328
Polymers287,1328
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59080 Å2
ΔGint-282.8 kcal/mol
Surface area94330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.084, 140.202, 165.226
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-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 25:345 )
211CHAIN B AND (RESSEQ 25:345 )
311CHAIN C AND (RESSEQ 25:345 )
411CHAIN D AND (RESSEQ 25:345 )
511CHAIN E AND (RESSEQ 25:345 )
611CHAIN F AND (RESSEQ 25:345 )
711CHAIN G AND (RESSEQ 25:345 )
811CHAIN H AND (RESSEQ 25:345 )

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Components

#1: Protein
PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA / WZA


Mass: 35891.547 Da / Num. of mol.: 8 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 22-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PBADHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LMG194 / References: UniProt: Q9X4B7

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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: 2.93 Å3/Da / Density % sol: 57.66 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.1, 0.2 M CACL2, 19% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.502
ReflectionResolution: 3→50 Å / Num. obs: 65664 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.8
Reflection shellHighest resolution: 3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J58

2j58


Resolution: 3→41.38 Å / σ(F): 1.33 / Phase error: 27.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.231 3313 5.1 %
Rwork0.21 --
obs0.211 64724 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.64 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9457 Å20 Å20 Å2
2---9.2458 Å20 Å2
3---9.7897 Å2
Refinement stepCycle: LAST / Resolution: 3→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19792 0 0 0 19792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820136
X-RAY DIFFRACTIONf_angle_d1.09327400
X-RAY DIFFRACTIONf_dihedral_angle_d16.2447288
X-RAY DIFFRACTIONf_chiral_restr0.0673192
X-RAY DIFFRACTIONf_plane_restr0.0053568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2466X-RAY DIFFRACTIONPOSITIONAL
12B2466X-RAY DIFFRACTIONPOSITIONAL0.043
13C2466X-RAY DIFFRACTIONPOSITIONAL0.046
14D2466X-RAY DIFFRACTIONPOSITIONAL0.044
15E2466X-RAY DIFFRACTIONPOSITIONAL0.037
16F2466X-RAY DIFFRACTIONPOSITIONAL0.047
17G2466X-RAY DIFFRACTIONPOSITIONAL0.04
18H2466X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9976-3.04930.38981520.34052814X-RAY DIFFRACTION98
3.0493-3.10470.36741860.31542964X-RAY DIFFRACTION98
3.1047-3.16440.28641700.25133022X-RAY DIFFRACTION98
3.1644-3.22890.2281810.21813089X-RAY DIFFRACTION98
3.2289-3.29910.24571640.20543073X-RAY DIFFRACTION98
3.2991-3.37580.23921600.20623104X-RAY DIFFRACTION98
3.3758-3.46020.2161630.20533074X-RAY DIFFRACTION98
3.4602-3.55370.20661440.19463140X-RAY DIFFRACTION98
3.5537-3.65820.25271510.21543072X-RAY DIFFRACTION98
3.6582-3.77620.24751670.22533064X-RAY DIFFRACTION98
3.7762-3.91110.22511830.21463039X-RAY DIFFRACTION98
3.9111-4.06760.24991520.20653041X-RAY DIFFRACTION98
4.0676-4.25250.22321490.19453059X-RAY DIFFRACTION98
4.2525-4.47650.24571640.20262961X-RAY DIFFRACTION98
4.4765-4.75660.19281620.18043020X-RAY DIFFRACTION98
4.7566-5.12320.19431720.19573069X-RAY DIFFRACTION98
5.1232-5.63760.22421750.21343102X-RAY DIFFRACTION98
5.6376-6.45070.21471610.20663172X-RAY DIFFRACTION98
6.4507-8.11720.19221600.20153209X-RAY DIFFRACTION98
8.1172-41.37970.20591680.19253352X-RAY DIFFRACTION98
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)
10.0777-0.016-0.00840.1068-0.02560.0599-0.09350.1751-0.0839-0.16960.0031-0.23660.0725-0.008-0.06570.166-0.00230.18020.1292-0.0850.0989-13.2291-48.632742.4471
20.13680.0183-0.01650.0277-0.00130.0612-0.08430.1889-0.163-0.11330.036-0.11550.0444-0.0475-0.05310.1999-0.05980.06510.1156-0.15490.0536-31.1023-60.906842.4167
30.02810.00170.02170.09880.04560.1061-0.07950.12620.1011-0.0884-0.03580.1605-0.0811-0.0015-0.07170.0935-0.0518-0.11890.18130.09820.0855-60.6685-17.730941.2884
40.05230.00920.01510.2164-0.07090.1468-0.09040.10930.0379-0.2278-0.0254-0.21510.07510.034-0.11110.0557-0.01930.13370.15490.0450.109-9.2387-27.361842.1067
50.1042-0.02120.0290.0223-0.03210.039-0.05190.14670.1924-0.1514-0.03-0.11180.01250.0664-0.04380.1736-0.05220.07980.12070.13440.1206-21.5272-9.494541.6872
60.08-0.0010.03630.13840.02760.0604-0.03940.17730.1911-0.1598-0.01390.108-0.02460.0501-0.08240.1396-0.0714-0.02810.12360.15950.0697-42.7335-5.492341.2975
70.0752-0.01650.01770.03030.04020.041-0.00470.1233-0.1435-0.1647-0.05210.09120.0231-0.053-0.06860.2385-0.0414-0.1050.1256-0.10730.0186-52.4153-56.936642.0597
80.0415-0.0346-0.03090.04040.03740.0833-0.10840.1289-0.0424-0.16990.01040.1765-0.03990.0144-0.05740.2032-0.1134-0.16770.1895-0.01660.1196-64.671-39.011741.6149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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