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- PDB-4e2c: Crystal Structure of the periplasmic domain of the chimeric LPS O... -

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Basic information

Entry
Database: PDB / ID: 4e2c
TitleCrystal Structure of the periplasmic domain of the chimeric LPS O-antigen chain length regulator protein
Componentschimeric WzzB Chain length determinant protein
KeywordsMEMBRANE PROTEIN / Chimeric polysaccharide co-polymerase / Bacterial inner membrane
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / identical protein binding / plasma membrane
Similarity search - Function
Bacterial polysaccharide co-polymerase-like / FepE-like / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chain length determinant protein / Chain length determinant protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Salmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKalynych, S. / Yao, D. / Magee, J.D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators.
Authors: Kalynych, S. / Yao, D. / Magee, J. / Cygler, M.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jul 5, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)55,4762
Polymers55,4762
Non-polymers00
Water1,49583
1
A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein

A: chimeric WzzB Chain length determinant protein
B: chimeric WzzB Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)221,9058
Polymers221,9058
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30600 Å2
ΔGint-145 kcal/mol
Surface area81230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.946, 116.946, 219.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein chimeric WzzB Chain length determinant protein / Polysaccharide antigen chain regulator


Mass: 27738.133 Da / Num. of mol.: 2 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria), (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: cld, rol, S2210, SF2089, wzzB, STM2079 / Plasmid: pF04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37792, UniProt: Q04866
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.0M Sodium Citrate, 5% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorDetector: CCD / Date: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 43.99 / Number: 151373 / Rmerge(I) obs: 0.064 / Χ2: 1.93 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 19253 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.595097.910.0332.5047.1
6.037.5910010.0412.3467.8
5.276.0399.910.0462.0758
4.795.2799.810.0442.1998
4.444.7999.710.0452.3918
4.184.4499.610.0542.6338
3.974.1899.810.0632.7498
3.83.9799.910.0662.268
3.653.899.810.0812.9967.2
3.533.659910.0842.0716.9
3.423.5310010.0811.628.1
3.323.4210010.0911.5488.2
3.233.3210010.1131.5678.2
3.153.2399.910.1351.4528.2
3.083.1599.910.151.4528.2
3.023.0810010.1731.4348.2
2.963.0299.910.1871.4138.2
2.92.9610010.2191.3418.3
2.852.910010.2291.2988.2
2.82.8599.610.2431.2366.4
ReflectionResolution: 2.8→50 Å / Num. obs: 23646 / % possible obs: 99.7 % / Observed criterion σ(I): 12.2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.926 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.856.40.2439221.236199.6
2.85-2.98.20.2299521.2981100
2.9-2.968.30.2199431.3411100
2.96-3.028.20.1879501.413199.9
3.02-3.088.20.1739581.4341100
3.08-3.158.20.159411.452199.9
3.15-3.238.20.1359431.452199.9
3.23-3.328.20.1139651.5671100
3.32-3.428.20.0919441.5481100
3.42-3.538.10.0819721.621100
3.53-3.656.90.0849362.071199
3.65-3.87.20.0819562.996199.8
3.8-3.9780.0669512.26199.9
3.97-4.1880.0639712.749199.8
4.18-4.4480.0549592.633199.6
4.44-4.7980.0459712.391199.7
4.79-5.2780.0449722.199199.8
5.27-6.0380.0469902.075199.9
6.03-7.597.80.04110032.3461100
7.59-507.10.03310542.504197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.5 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.296 1182 RANDOM
Rwork0.235 --
obs-19253 -
Displacement parametersBiso max: 156.14 Å2 / Biso mean: 30.7549 Å2 / Biso min: 3.73 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 83 3585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.14

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