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- PDB-3b8p: Fragment of WzzB, Polysaccharide Co-polymerase from Salmonella Ty... -

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Basic information

Entry
Database: PDB / ID: 3b8p
TitleFragment of WzzB, Polysaccharide Co-polymerase from Salmonella Typhimurium
ComponentsChain length determinant protein
KeywordsMEMBRANE PROTEIN / WZZ / WzzB / Bacterial Polysaccharide Co-polymerase / Inner membrane / Lipopolysaccharide biosynthesis / Membrane / Transmembrane
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
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsTocilj, A. / Matte, A. / Cygler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Bacterial polysaccharide co-polymerases share a common framework for control of polymer length
Authors: Tocilj, A. / Munger, C. / Proteau, A. / Morona, R. / Purins, L. / Ajamian, E. / Wagner, J. / Papadopoulos, M. / Van Den Bosch, L. / Rubinstein, J.L. / Fethiere, J. / Matte, A. / Cygler, M.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,2925
Polymers137,2925
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)27,4581
Polymers27,4581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)27,4581
Polymers27,4581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)27,4581
Polymers27,4581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)27,4581
Polymers27,4581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Chain length determinant protein


Theoretical massNumber of molelcules
Total (without water)27,4581
Polymers27,4581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.972, 112.744, 170.929
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 6

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUAA54 - 2923 - 241
2LYSLYSBB55 - 2924 - 241
3GLUGLUCC54 - 2923 - 241
4GLUGLUDD54 - 2923 - 241
5GLUGLUEE54 - 2923 - 241

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Components

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


Mass: 27458.379 Da / Num. of mol.: 5 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: wzzB, cld, rol / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04866
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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 200mM MgCl, 100mM Nacacodylate pH 6.5, 20%PEG 8000, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→29.31 Å / Num. obs: 27458 / % possible obs: 99.9 % / Redundancy: 7.36 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3-3.317.460.3344.51100
3.31-3.457.420.2585.41100
3.45-3.67.410.1996.71100
3.6-3.797.370.1478.7199.9
3.79-4.037.350.10911.61100
4.03-4.347.40.07515.81100
4.34-4.787.430.05620.51100
4.78-5.467.380.05520.71100
5.46-6.877.280.05620199.9
6.87-29.317.130.04424.7199.8

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1003.329.2823555885
ANO_10.9503.329.28230590
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_113.25-29.280032045
ISO_19.89-13.250049650
ISO_18.23-9.890063546
ISO_17.2-8.230074442
ISO_16.48-7.20084344
ISO_15.94-6.480093036
ISO_15.51-5.9400102437
ISO_15.17-5.5100109745
ISO_14.88-5.1700116435
ISO_14.64-4.8800123143
ISO_14.43-4.6400130132
ISO_14.24-4.4300134549
ISO_14.08-4.2400141739
ISO_13.93-4.0800145555
ISO_13.8-3.9300150540
ISO_13.68-3.800159944
ISO_13.58-3.6800157355
ISO_13.48-3.5800166850
ISO_13.38-3.4800161942
ISO_13.3-3.3800158956
ANO_113.25-29.280.5303200
ANO_19.89-13.250.60104960
ANO_18.23-9.890.64806350
ANO_17.2-8.230.68307440
ANO_16.48-7.20.71408430
ANO_15.94-6.480.75909290
ANO_15.51-5.940.824010240
ANO_15.17-5.510.831010970
ANO_14.88-5.170.874011620
ANO_14.64-4.880.909012290
ANO_14.43-4.640.921013010
ANO_14.24-4.430.942013450
ANO_14.08-4.240.961014170
ANO_13.93-4.080.979014540
ANO_13.8-3.930.983015030
ANO_13.68-3.80.988015980
ANO_13.58-3.680.993015520
ANO_13.48-3.580.995016030
ANO_13.38-3.480.997014940
ANO_13.3-3.380.999013130
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
11.017-72.541-79.648SE102.440.15
2-4.853-98.668-76.166SE65.690.12
3-26.958-100.21-60.118SE96.890.11
4-34.924-75.084-54.657SE71.450.1
5-17.86-57.796-66.999SE78.090.09
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.63 / Reflection: 28847 / Reflection acentric: 27697 / Reflection centric: 1150
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-29.2820.940.950.8414361291145
5.4-8.60.810.820.7344244187237
4.3-5.40.810.810.7355665335231
3.8-4.30.680.680.6655655373192
3.2-3.80.440.440.4592268953273
3-3.20.20.190.222630255872

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Processing

Software
NameVersionClassificationNB
d*TREK9.6Ldata scaling
SHARPphasing
RESOLVE2.13phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.1→29.24 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.848 / SU B: 19.112 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.481
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 5 REMARK 5 WARNING REMARK 5 DATA QUALITY, DYNAMIC DISORDER AND HIGH ANISOTROPICITY REMARK 5 LIMIT THE QUALITY OF THE FINAL REFINED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 5 REMARK 5 WARNING REMARK 5 DATA QUALITY, DYNAMIC DISORDER AND HIGH ANISOTROPICITY REMARK 5 LIMIT THE QUALITY OF THE FINAL REFINED MODEL REMARK 5 REMARK 5 PENTAMERIC ARRANGEMENT IN ASU MIGHT NOT RESEMBLE BIOLOGICAL UNIT REMARK 5
RfactorNum. reflection% reflectionSelection details
Rfree0.30149 1416 5.1 %RANDOM
Rwork0.25462 ---
obs0.25699 26547 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.18 Å2
2--0.45 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 0 0 6778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226868
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3941.9569427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.065930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65626.075265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33415976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.691522
X-RAY DIFFRACTIONr_chiral_restr0.160.21197
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.33344
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.54888
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.5387
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.070.38
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.12744820
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.67887499
X-RAY DIFFRACTIONr_scbond_it5.49252327
X-RAY DIFFRACTIONr_scangle_it9.068101928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1153 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.645
2Bloose positional0.735
3Cloose positional0.845
4Dloose positional0.595
5Eloose positional0.95
1Aloose thermal5.3710
2Bloose thermal6.4110
3Cloose thermal4.2710
4Dloose thermal5.8510
5Eloose thermal5.4710
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 51 -
Rwork0.355 1036 -
obs--100 %

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