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- PDB-4e2h: Crystal structure of the periplasmic domain of Shigella flexneri WzzB -

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Basic information

Entry
Database: PDB / ID: 4e2h
TitleCrystal structure of the periplasmic domain of Shigella flexneri WzzB
ComponentsChain length determinant protein
KeywordsMEMBRANE PROTEIN / Wzz / LPS O-antigen chain length determination / inner membrane / periplasmic space
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / 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
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.36 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chain length determinant protein
C: Chain length determinant protein
B: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)82,5063
Polymers82,5063
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-36 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.514, 62.619, 90.740
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27502.115 Da / Num. of mol.: 3 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: wzzB, cld, rol, SF2089, S2210 / Plasmid: pFO4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37792
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 0.1M Hepes, 0.1M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97912 Å
DetectorDate: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.36→49.7 Å / Num. all: 24179 / Num. obs: 22670 / % possible obs: 94 % / Observed criterion σ(I): 22.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.36→49.597 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7178 / SU ML: 0.38 / σ(F): 2 / Phase error: 34.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 1509 5.12 %Random
Rwork0.2454 ---
obs0.2483 22670 77.96 %-
all-24179 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.383 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 157.84 Å2 / Biso mean: 52.9407 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-18.672 Å2-0 Å2-2.6039 Å2
2---3.098 Å20 Å2
3----15.5741 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 0 78 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015000
X-RAY DIFFRACTIONf_angle_d1.3946795
X-RAY DIFFRACTIONf_chiral_restr0.09809
X-RAY DIFFRACTIONf_plane_restr0.007896
X-RAY DIFFRACTIONf_dihedral_angle_d20.1941832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.43690.3627690.3381273134239
2.4369-2.5240.3767770.33871665174251
2.524-2.6250.3721000.32441939203960
2.625-2.74450.38351320.29992225235769
2.7445-2.88910.34271400.2762464260477
2.8891-3.07010.31291410.26452677281882
3.0701-3.30710.32731580.27112923308190
3.3071-3.63990.32881490.24553097324694
3.6399-4.16630.27691710.21323171334297
4.1663-5.24820.25811820.20593211339398
5.2482-49.60770.2831900.23273318350899

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