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- PDB-7xfd: Polysaccharide export protein Wza -

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Basic information

Entry
Database: PDB / ID: 7xfd
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: 2.2 Å
AuthorsZheng, J. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21773014 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


Theoretical massNumber of molelcules
Total (without water)40,8072
Polymers40,8072
Non-polymers00
Water6,143341
1
A: Polysaccharide export protein
B: Polysaccharide export protein

A: Polysaccharide export protein
B: Polysaccharide export protein

A: Polysaccharide export protein
B: Polysaccharide export protein

A: Polysaccharide export protein
B: Polysaccharide export protein


Theoretical massNumber of molelcules
Total (without water)163,2308
Polymers163,2308
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area25190 Å2
ΔGint-86 kcal/mol
Surface area52070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.895, 96.895, 220.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-469-

HOH

31A-471-

HOH

41B-428-

HOH

51B-451-

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.: 2
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.: 341 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Potassium phosphate monobasic, pH 7.3, 5% glycerol
PH range: 7.3

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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: 2.2→29.52 Å / Num. obs: 27007 / % possible obs: 98.57 % / Redundancy: 5 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.8 / Net I/σ(I): 0.8
Reflection shellResolution: 2.2→2.279 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: 2.2→29.52 Å / SU ML: 0.3261 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2879 1976 7.4 %
Rwork0.265 24732 -
obs0.2666 26708 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 0 341 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562718
X-RAY DIFFRACTIONf_angle_d0.81583714
X-RAY DIFFRACTIONf_chiral_restr0.0574418
X-RAY DIFFRACTIONf_plane_restr0.0053492
X-RAY DIFFRACTIONf_dihedral_angle_d14.2566378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.47261220.4711550X-RAY DIFFRACTION88.56
2.26-2.320.4521360.39831715X-RAY DIFFRACTION97.63
2.32-2.380.28811400.28021745X-RAY DIFFRACTION99.89
2.38-2.460.35751410.27971772X-RAY DIFFRACTION100
2.46-2.550.27631430.27681783X-RAY DIFFRACTION99.9
2.55-2.650.29031400.27521743X-RAY DIFFRACTION99.95
2.65-2.770.3471420.29331774X-RAY DIFFRACTION99.74
2.77-2.920.3211390.26291760X-RAY DIFFRACTION99.74
2.92-3.10.261430.26271775X-RAY DIFFRACTION99.33
3.1-3.340.27111410.26151783X-RAY DIFFRACTION99.12
3.34-3.670.28271420.24311772X-RAY DIFFRACTION99.27
3.68-4.20.2621450.23211785X-RAY DIFFRACTION98.82
4.21-5.290.2271470.21011838X-RAY DIFFRACTION99.6
5.29-29.520.24061550.22661937X-RAY DIFFRACTION99.38

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