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- PDB-7xff: Polysaccharide export protein Wza -

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Basic information

Entry
Database: PDB / ID: 7xff
TitlePolysaccharide export protein Wza
ComponentsPolysaccharide export protein
KeywordsMEMBRANE PROTEIN / polysaccharide export protein
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 / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / : / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / : ...wza like fold / wza like domain / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / : / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / : / SLBB domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polysaccharide export protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZheng, J. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Polysaccharide export protein Wza
Authors: Wang, B. / Zheng, J.
History
DepositionApr 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polysaccharide export protein
B: Polysaccharide export protein
C: Polysaccharide export protein
D: Polysaccharide export protein
E: Polysaccharide export protein
F: Polysaccharide export protein
G: Polysaccharide export protein
H: Polysaccharide export protein


Theoretical massNumber of molelcules
Total (without water)163,2308
Polymers163,2308
Non-polymers00
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27320 Å2
ΔGint-101 kcal/mol
Surface area56190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.768, 193.039, 106.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein
Polysaccharide export protein / Polysaccharide export protein Wza / Putative polysaccharide export protein


Mass: 20403.742 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: wza, A5U30_002223, A8499_004210, BON78_05920, BON79_06745, BR158_000680, CCV12_003719, CT143_03515, D3G36_16900, D4U49_08845, D9E49_15345, E2646_01750, E3O05_07155, ELT23_04100, ELT31_04920, ...Gene: wza, A5U30_002223, A8499_004210, BON78_05920, BON79_06745, BR158_000680, CCV12_003719, CT143_03515, D3G36_16900, D4U49_08845, D9E49_15345, E2646_01750, E3O05_07155, ELT23_04100, ELT31_04920, ELT38_06380, ELT50_04065, ELT52_20945, ELT56_02735, ELU95_02210, ELV05_05145, ELY31_02030, GF147_02635, HMW38_04280, IFB95_000024, NCTC10089_01822, NCTC9075_02568
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0V9R7J8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.05 M Potassium phosphate monobasic, pH 7.3, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.988 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Oct 16, 2021
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.3→26.63 Å / Num. obs: 76600 / % possible obs: 83.77 % / Redundancy: 5 % / Biso Wilson estimate: 29.47 Å2 / CC1/2: 0.8 / Net I/σ(I): 0.8
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 7 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J58

2j58


Resolution: 2.3→26.63 Å / SU ML: 0.2829 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.6677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1865 2.62 %
Rwork0.1837 69398 -
obs0.1849 71263 83.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11428 0 0 877 12305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009311659
X-RAY DIFFRACTIONf_angle_d1.217415929
X-RAY DIFFRACTIONf_chiral_restr0.06211804
X-RAY DIFFRACTIONf_plane_restr0.00882115
X-RAY DIFFRACTIONf_dihedral_angle_d15.33861622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.2355940.20923144X-RAY DIFFRACTION50.02
2.36-2.430.28181010.21323533X-RAY DIFFRACTION56.09
2.43-2.510.30331100.21384147X-RAY DIFFRACTION65.55
2.51-2.60.26581280.214570X-RAY DIFFRACTION72.35
2.6-2.70.261400.2175088X-RAY DIFFRACTION81.12
2.7-2.830.2611460.21015583X-RAY DIFFRACTION87.9
2.83-2.970.25471550.19595866X-RAY DIFFRACTION92.39
2.97-3.160.22251560.1866006X-RAY DIFFRACTION94.76
3.16-3.40.24421630.186145X-RAY DIFFRACTION96.63
3.4-3.750.19891710.17486272X-RAY DIFFRACTION98.37
3.75-4.290.21251700.16086365X-RAY DIFFRACTION99.09
4.29-5.390.2131640.1676406X-RAY DIFFRACTION99.52
5.39-26.630.21581670.18856273X-RAY DIFFRACTION94.32

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