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- PDB-4wl1: Structure of WzzE Polysaccharide Co-polymerase -

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Basic information

Entry
Database: PDB / ID: 4wl1
TitleStructure of WzzE Polysaccharide Co-polymerase
ComponentsLipopolysaccharide biosynthesis protein WzzE
KeywordsMEMBRANE PROTEIN / ECA / Enterobacterial common antigen / chain length regulator / polysaccharide co-polymerase
Function / homologyECA polysaccharide chain length modulation protein WzzE / enterobacterial common antigen biosynthetic process / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / identical protein binding / plasma membrane / ECA polysaccharide chain length modulation protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.989 Å
AuthorsKalynych, S. / Cherney, M. / Cygler, M.
CitationJournal: Protein Sci. / Year: 2015
Title: Quaternary structure of WzzB and WzzE polysaccharide copolymerases.
Authors: Kalynych, S. / Cherney, M. / Bostina, M. / Rouiller, I. / Cygler, M.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharide biosynthesis protein WzzE
B: Lipopolysaccharide biosynthesis protein WzzE
C: Lipopolysaccharide biosynthesis protein WzzE
D: Lipopolysaccharide biosynthesis protein WzzE
E: Lipopolysaccharide biosynthesis protein WzzE
F: Lipopolysaccharide biosynthesis protein WzzE
G: Lipopolysaccharide biosynthesis protein WzzE
H: Lipopolysaccharide biosynthesis protein WzzE
I: Lipopolysaccharide biosynthesis protein WzzE
J: Lipopolysaccharide biosynthesis protein WzzE
K: Lipopolysaccharide biosynthesis protein WzzE
L: Lipopolysaccharide biosynthesis protein WzzE
M: Lipopolysaccharide biosynthesis protein WzzE
N: Lipopolysaccharide biosynthesis protein WzzE
O: Lipopolysaccharide biosynthesis protein WzzE
P: Lipopolysaccharide biosynthesis protein WzzE
Q: Lipopolysaccharide biosynthesis protein WzzE
R: Lipopolysaccharide biosynthesis protein WzzE
S: Lipopolysaccharide biosynthesis protein WzzE
T: Lipopolysaccharide biosynthesis protein WzzE
U: Lipopolysaccharide biosynthesis protein WzzE
V: Lipopolysaccharide biosynthesis protein WzzE
W: Lipopolysaccharide biosynthesis protein WzzE
X: Lipopolysaccharide biosynthesis protein WzzE
Y: Lipopolysaccharide biosynthesis protein WzzE
Z: Lipopolysaccharide biosynthesis protein WzzE
a: Lipopolysaccharide biosynthesis protein WzzE
b: Lipopolysaccharide biosynthesis protein WzzE
c: Lipopolysaccharide biosynthesis protein WzzE
d: Lipopolysaccharide biosynthesis protein WzzE
e: Lipopolysaccharide biosynthesis protein WzzE
f: Lipopolysaccharide biosynthesis protein WzzE


Theoretical massNumber of molelcules
Total (without water)1,296,16132
Polymers1,296,16132
Non-polymers00
Water0
1
A: Lipopolysaccharide biosynthesis protein WzzE
B: Lipopolysaccharide biosynthesis protein WzzE
C: Lipopolysaccharide biosynthesis protein WzzE
D: Lipopolysaccharide biosynthesis protein WzzE
E: Lipopolysaccharide biosynthesis protein WzzE
F: Lipopolysaccharide biosynthesis protein WzzE
G: Lipopolysaccharide biosynthesis protein WzzE
H: Lipopolysaccharide biosynthesis protein WzzE


Theoretical massNumber of molelcules
Total (without water)324,0408
Polymers324,0408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-60 kcal/mol
Surface area89330 Å2
MethodPISA
2
I: Lipopolysaccharide biosynthesis protein WzzE
J: Lipopolysaccharide biosynthesis protein WzzE
K: Lipopolysaccharide biosynthesis protein WzzE
L: Lipopolysaccharide biosynthesis protein WzzE
M: Lipopolysaccharide biosynthesis protein WzzE
N: Lipopolysaccharide biosynthesis protein WzzE
O: Lipopolysaccharide biosynthesis protein WzzE
P: Lipopolysaccharide biosynthesis protein WzzE


Theoretical massNumber of molelcules
Total (without water)324,0408
Polymers324,0408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17930 Å2
ΔGint-57 kcal/mol
Surface area89210 Å2
MethodPISA
3
Q: Lipopolysaccharide biosynthesis protein WzzE
R: Lipopolysaccharide biosynthesis protein WzzE
S: Lipopolysaccharide biosynthesis protein WzzE
T: Lipopolysaccharide biosynthesis protein WzzE
U: Lipopolysaccharide biosynthesis protein WzzE
V: Lipopolysaccharide biosynthesis protein WzzE
W: Lipopolysaccharide biosynthesis protein WzzE
X: Lipopolysaccharide biosynthesis protein WzzE


Theoretical massNumber of molelcules
Total (without water)324,0408
Polymers324,0408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-57 kcal/mol
Surface area89110 Å2
MethodPISA
4
Y: Lipopolysaccharide biosynthesis protein WzzE
Z: Lipopolysaccharide biosynthesis protein WzzE
a: Lipopolysaccharide biosynthesis protein WzzE
b: Lipopolysaccharide biosynthesis protein WzzE
c: Lipopolysaccharide biosynthesis protein WzzE
d: Lipopolysaccharide biosynthesis protein WzzE
e: Lipopolysaccharide biosynthesis protein WzzE
f: Lipopolysaccharide biosynthesis protein WzzE


Theoretical massNumber of molelcules
Total (without water)324,0408
Polymers324,0408
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18530 Å2
ΔGint-61 kcal/mol
Surface area88580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.849, 246.306, 133.201
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
Lipopolysaccharide biosynthesis protein WzzE


Mass: 40505.016 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: wzzE, wzz, Z5296, ECs4718 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P0AG01

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 8% PEG 8000, 0.1M Bis-Tris pH 6.5, 0.2M NaCl, 15% glycerol
Temp details: 22C - Room temperature

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 5.99→47.81 Å / Num. all: 43381 / Num. obs: 43381 / % possible obs: 96.38 % / Redundancy: 3.5 % / Net I/σ(I): 11.73
Reflection shellResolution: 5.9→6.2 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.15 / % possible all: 83.54

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B8O

3b8o


Resolution: 5.989→47.81 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2455 2205 5.08 %
Rwork0.234 --
obs0.2369 43379 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.989→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57504 0 0 0 57504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01258560
X-RAY DIFFRACTIONf_angle_d2.24879200
X-RAY DIFFRACTIONf_dihedral_angle_d18.85122144
X-RAY DIFFRACTIONf_chiral_restr0.2758512
X-RAY DIFFRACTIONf_plane_restr0.00910496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.9923-6.13120.27261130.2942297X-RAY DIFFRACTION77
6.1312-6.2840.30951400.29672655X-RAY DIFFRACTION89
6.284-6.45320.29161270.29552709X-RAY DIFFRACTION91
6.4532-6.64230.30511380.28112768X-RAY DIFFRACTION93
6.6423-6.85570.271380.27572772X-RAY DIFFRACTION94
6.8557-7.09940.28361660.26982801X-RAY DIFFRACTION94
7.0994-7.3820.2451410.25122849X-RAY DIFFRACTION95
7.382-7.71570.27851530.24422836X-RAY DIFFRACTION95
7.7157-8.11940.23281490.23052790X-RAY DIFFRACTION95
8.1194-8.62340.20961280.21952859X-RAY DIFFRACTION96
8.6234-9.28160.20871560.20212840X-RAY DIFFRACTION95
9.2816-10.20190.19671790.19922809X-RAY DIFFRACTION93
10.2019-11.64660.20781620.19312768X-RAY DIFFRACTION92
11.6466-14.5570.23861420.19242748X-RAY DIFFRACTION91
14.557-40.22520.31381380.29322663X-RAY DIFFRACTION87

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