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- PDB-4e29: Periplasmic domain of the chimeric WzzB chain length regulator protein -

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Basic information

Entry
Database: PDB / ID: 4.0E+29
TitlePeriplasmic domain of the chimeric WzzB chain length regulator protein
ComponentsChimeric WzzB chain length determinant protein
KeywordsMEMBRANE PROTEIN / Wzz / Regulation of LPS O-antigen chain length / 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 / AB INITIO PHASING / Resolution: 1.6 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 7, 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 1.4Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)56,6462
Polymers56,6462
Non-polymers00
Water14,232790
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)226,5848
Polymers226,5848
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 area31230 Å2
ΔGint-130 kcal/mol
Surface area80520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.757, 115.757, 210.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-601-

HOH

21B-680-

HOH

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Components

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


Mass: 28323.027 Da / Num. of mol.: 2 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Details: IPTG-inducible pET based E.coli expression vector
Source: (gene. exp.) Shigella flexneri (bacteria), (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: cld, rol, S2210, SF2089, wzzB, STM2079 / Plasmid: pFO4 / 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.: 790 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: NaFormate, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.96406 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96406 Å / Relative weight: 1
ReflectionResolution: 1.6→32.698 Å / Num. all: 94818 / Num. obs: 90288 / Observed criterion σ(I): 11

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→32.698 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.18 / σ(F): 0 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 4557 5.05 %
Rwork0.2178 --
obs0.2189 90287 96.01 %
all-94818 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.923 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.391 Å20 Å2-0 Å2
2--1.391 Å2-0 Å2
3----2.782 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 790 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063562
X-RAY DIFFRACTIONf_angle_d0.9234844
X-RAY DIFFRACTIONf_dihedral_angle_d13.2481310
X-RAY DIFFRACTIONf_chiral_restr0.056585
X-RAY DIFFRACTIONf_plane_restr0.004627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.28144120.23377946X-RAY DIFFRACTION90
1.6572-1.72350.25534170.22998094X-RAY DIFFRACTION92
1.7235-1.8020.24944580.22868279X-RAY DIFFRACTION94
1.802-1.8970.26694330.23218399X-RAY DIFFRACTION95
1.897-2.01580.24964280.23038404X-RAY DIFFRACTION95
2.0158-2.17140.245170.20788716X-RAY DIFFRACTION99
2.1714-2.38990.23014750.20738692X-RAY DIFFRACTION98
2.3899-2.73560.25964770.23038894X-RAY DIFFRACTION99
2.7356-3.44590.24284600.21989017X-RAY DIFFRACTION100
3.4459-32.70530.20884800.20729290X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24950.39440.25190.82990.49170.52190.0868-0.0033-0.0927-0.23620.03220.18740.236-0.0177-0.1080.40980.0271-0.20110.0729-0.01470.199625.931355.781529.2888
20.03380.03170.10550.2322-0.06630.3246-0.0310.01310.0479-0.1275-0.04460.0627-0.04830.0370.06550.11360.0256-0.04170.0647-0.01080.082238.586244.641868.3487
31.11470.41211.20060.63160.99481.9091-0.16440.1844-0.1606-0.10540.3088-0.097-0.29980.4514-0.17340.1143-0.0778-0.0080.1738-0.06640.119236.91934.194329.4679
40.44450.23950.87570.09890.33131.0277-0.0590.09160.0043-0.05920.00530.0296-0.14370.06650.02610.08330.0166-0.01010.1559-0.03320.090653.366334.677468.0465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 55:161)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 162:291)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 55:160)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 161:289)

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