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- PDB-3b8o: Structure of WzzE- Bacterial Polysaccharide Co-polymerase -

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Basic information

Entry
Database: PDB / ID: 3b8o
TitleStructure of WzzE- Bacterial Polysaccharide Co-polymerase
ComponentsLipopolysaccharide biosynthesis protein wzzE
KeywordsBIOSYNTHETIC PROTEIN / WZZ / WzzE / Bacterial Polysaccharide Co-polymerase / Inner membrane / Lipopolysaccharide biosynthesis / Membrane / Transmembrane / MEMBRANE PROTEIN
Function / homology
Function and homology information


enterobacterial common antigen biosynthetic process / identical protein binding / plasma membrane
Similarity search - Function
Bacterial polysaccharide co-polymerase-like / FepE-like / ECA polysaccharide chain length modulation protein WzzE / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ECA polysaccharide chain length modulation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Apr 18, 2012Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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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


Theoretical massNumber of molelcules
Total (without water)247,3128
Polymers247,3128
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.438, 108.299, 122.569
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A
14E
24A
15F
25A
16G
26A
17H
27A

NCS domain segments:

Component-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 55 - 319 / Label seq-ID: 1 - 265

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA
13DD
23AA
14EE
24AA
15FF
25AA
16GG
26AA
17HH
27AA

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
Lipopolysaccharide biosynthesis protein wzzE


Mass: 30913.971 Da / Num. of mol.: 8 / Fragment: Periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: wzzE, wzz / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AG01
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 298 K / pH: 7
Details: PEG 3350, pH 7.0, vapor diffusion, temperature 298K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 117899 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.297 / % possible all: 78.8

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.3939.41969203205
ANO_10.75902.3939.41946890
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_110.34-39.41001200165
ISO_17.44-10.34002149179
ISO_16.11-7.44002752173
ISO_15.31-6.11003280178
ISO_14.76-5.31003711173
ISO_14.35-4.76004107178
ISO_14.03-4.35004469175
ISO_13.77-4.03004849177
ISO_13.56-3.77005044171
ISO_13.37-3.56005417171
ISO_13.22-3.37005686180
ISO_13.08-3.22005972173
ISO_12.96-3.08006219179
ISO_12.86-2.96006469173
ISO_12.76-2.86006655177
ISO_12.67-2.76006812174
ISO_12.59-2.67006708138
ISO_12.52-2.59005890115
ISO_12.45-2.5200518087
ISO_12.39-2.4500435169
ANO_110.34-39.410.349011870
ANO_17.44-10.340.33021430
ANO_16.11-7.440.345027460
ANO_15.31-6.110.374032800
ANO_14.76-5.310.423037060
ANO_14.35-4.760.46041050
ANO_14.03-4.350.521044680
ANO_13.77-4.030.582048460
ANO_13.56-3.770.682050260
ANO_13.37-3.560.683054140
ANO_13.22-3.370.732056800
ANO_13.08-3.220.781059580
ANO_12.96-3.080.824061970
ANO_12.86-2.960.861064210
ANO_12.76-2.860.894065580
ANO_12.67-2.760.919066520
ANO_12.59-2.670.944063840
ANO_12.52-2.590.958054320
ANO_12.45-2.520.964046460
ANO_12.39-2.450.971038400
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
136.55197.06371.671SE28.370.13
270.24591.3550.169SE27.570.12
390.996112.02650.033SE30.190.13
431.326117.17269.83SE44.610.13
561.653130.764114.64SE58.430.15
672.891106.03772.225SE27.270.12
799.39296.69328.414SE51.380.12
845.202130.54484.813SE51.130.12
993.423132.04170.052SE45.160.11
1077.212143.015114.705SE58.80.13
1178.11285.85170.087SE440.14
1265.268112.13669.433SE31.030.1
1370.974135.05796.646SE50.460.12
1449.851121.07391.064SE49.480.12
15102.622132.89973.133SE29.070.11
1632.685143.213116.158SE55.670.12
1751.347129.35396.578SE48.630.11
1865.822125.48249.441SE30.160.1
1985.276119.89948.087SE38.240.1
207.974126.866124.733SE62.010.14
21-3.511136.447148.293SE45.780.1
2279.49149.447116.065SE77.410.14
2341.943133.72114.49SE51.410.12
24107.74397.99822.953SE56.060.12
2574.873124.77546.329SE26.970.09
2628.315159.20196.77SE48.360.12
2723.579114.499124.843SE56.170.14
2877.52895.16973.648SE26.240.09
29-8.405126.857154.576SE53.470.12
3044.15391.10569.411SE33.260.09
3127.643136.72290.43SE71.520.13
3225.839108.002123.641SE59.920.11
3332.101107.86473.291SE37.630.1
34-25.952120.456148.897SE58.260.13
3529.425149.141114.664SE65.640.14
3613.901123.63123.296SE61.780.1
3717.347122.434142.888SE51.380.1
38-28.301112.828154.6SE29.020.07
39-11.611123.713124.93SE63.780.12
40-20.87114.25123.479SE59.560.11
4125.348144.50384.764SE18.210.06
42-2.116128.109142.821SE45.60.1
43-24.138108.281124.85SE59.790.12
4419.745160.56391.446SE54.590.1
4567.523133.869116.133SE47.20.09
4675.78283.57648.407SE21.440.07
4748.302131.602116.011SE66.710.11
48108.87491.71134.661SE64.260.1
4973.501128.25891.041SE28.480.07
5019.974129.05148.689SE78.220.11
51-5.205125.922123.469SE78.90.11
52109.454121.78385.793SE100.990.08
53-27.647139.11141.162SE115.650.13
5429.119165.80784.993SE60.850.09
5521.589100.91785.722SE68.940.08
5692.111126.2298.519SE106.170.1
5781.577135.72133.802SE740.07
5888.1102.27685.725SE107.50.11
5966.245126.3784.872SE39.450.05
6026.187118.20598.341SE105.020.12
6179.246106.83398.226SE113.950.11
62-18.978117.22143.669SE138.380.11
63113.985130.90998.141SE93.110.1
6430.53396.31198.379SE113.550.12
6534.59140.15695.77SE109.350.1
6686.327126.4221.49SE140.40.13
6712.732131.269154.511SE34.540.06
6865.89122.02485.602SE58.060.06
6938.15218.86334.128SE56.530.04
7064.22122.43621.466SE58.430.06
7133.94733.6192.981SE54.760.03
729.55811.2496.635SE60.630.1
Phasing dmFOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.61 / Reflection: 83750 / Reflection acentric: 80833 / Reflection centric: 2917
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-29.9240.930.940.8336803341339
4.6-7.40.890.890.721128310712571
3.7-4.60.880.890.751409713578519
3.3-3.70.830.830.711425213806446
2.8-3.30.620.620.452524224550692
2.6-2.80.40.410.241519614846350

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHARPphasing
RESOLVE2.13phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.89 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.903 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26562 5290 5 %RANDOM
Rwork0.22333 ---
obs0.22546 101074 99.06 %-
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: 54.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14376 0 0 395 14771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.94219800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73551744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63124.216816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.111152536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46215144
X-RAY DIFFRACTIONr_chiral_restr0.0930.22128
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.26843
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.210046
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.84939098
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.765614184
X-RAY DIFFRACTIONr_scbond_it2.9346379
X-RAY DIFFRACTIONr_scangle_it4.45985616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 1797 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Bmedium positional0.390.5
2Cmedium positional0.270.5
3Dmedium positional0.320.5
4Emedium positional0.250.5
5Fmedium positional0.390.5
6Gmedium positional0.270.5
7Hmedium positional0.360.5
1Bmedium thermal0.852
2Cmedium thermal0.72
3Dmedium thermal0.762
4Emedium thermal0.782
5Fmedium thermal0.792
6Gmedium thermal0.72
7Hmedium thermal0.722
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 343 -
Rwork0.241 7112 -
obs--93.97 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.3511-2.88820.69972.79410.15463.6985-0.06050.0125-0.18770.13610.05990.31540.0369-0.22520.0006-0.20530.0102-0.0265-0.1970.0115-0.093956.14516.40644.018
20.1280.63151.36233.13716.508716.5009-0.22270.23430.1352-0.57480.141-0.0955-0.291-0.04130.08170.3191-0.0356-0.01450.2248-0.02250.032853.2992.2674.859
32.4568-0.33390.10364.5154-0.70991.6532-0.0653-0.2343-0.0126-0.054-0.01770.041-0.2061-0.11980.0829-0.18980.0189-0.0086-0.1612-0.0216-0.160763.421-10.58344.285
42.96911.895.04121.83394.803412.5888-0.07750.4503-0.0817-0.41270.0389-0.0587-0.39460.16010.03860.4204-0.0023-0.05830.0804-0.022-0.039452.062-18.8424.941
52.84651.9286-0.51454.4249-0.84622.8375-0.0239-0.09170.04910.03160.0132-0.0434-0.1438-0.03340.0107-0.2226-0.00920.0152-0.1646-0.0077-0.119149.387-35.67444.334
63.7369-0.95046.12090.3918-0.7514.36360.14720.7185-0.0536-0.3096-0.317-0.0686-0.06460.29510.16980.1342-0.01360.02820.3476-0.01360.011135.566-32.635.038
73.01430.3853-0.74511.8666-0.61322.9142-0.04180.04230.02120.21180.0543-0.0085-0.24420.1137-0.0125-0.19790.03370.0289-0.1833-0.0007-0.127622.53-43.45444.181
81.7935-1.95784.51873.1187-4.818511.39790.04290.4325-0.1969-0.4860.10760.16060.09420.2031-0.15050.0699-0.07530.00230.3430.0366-0.003914.505-31.6454.924
93.1333-1.6665-0.29652.7451-0.26113.6284-0.0295-0.04590.09180.00930.0032-0.14680.00680.21820.0263-0.23630.04240.006-0.1839-0.0032-0.1677-2.269-29.57344.014
100.34920.797-1.28222.8041-5.940616.3228-0.21050.3139-0.0858-0.61980.103-0.00050.1572-0.03440.10740.3049-0.0080.02020.14660.0111-0.04410.464-15.5524.803
111.5895-0.4509-0.45493.11790.78241.76410.007-0.13890.0616-0.0818-0.0245-0.01570.14770.21490.0175-0.22670.0123-0.0015-0.1519-0.0125-0.1631-9.615-2.60644.197
122.87661.921-4.91171.696-4.438911.63690.03060.45960.1796-0.34670.04460.04060.0798-0.1584-0.07510.46760.07420.0920.12150.0536-0.00831.7845.5364.84
132.60842.4220.06473.14840.0032.77310.0407-0.0969-0.04910.0765-0.0539-0.04870.17190.07760.0132-0.2075-0.03440.0005-0.1178-0.0121-0.08144.47422.2244.011
144.4755-1.1605-5.79450.43940.66412.57820.28270.85890.1739-0.3373-0.38550.0071-0.1588-0.18130.10280.16820.00240.03280.41110.02530.04118.18419.4174.852
153.58130.59870.95782.57520.94322.62770.01420.0576-0.00590.2495-0.0297-0.06820.2436-0.22130.0155-0.2069-0.0008-0.0041-0.14310.0415-0.104731.23530.12844.168
161.6416-2.0206-4.58243.45295.607212.79280.11190.36140.1842-0.55410.1453-0.2431-0.2306-0.3834-0.25720.0711-0.10220.02130.4073-0.02070.050339.34618.4464.808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA55 - 651 - 11
2X-RAY DIFFRACTION1AA95 - 18141 - 127
3X-RAY DIFFRACTION1AA307 - 319253 - 265
4X-RAY DIFFRACTION2AA66 - 8512 - 31
5X-RAY DIFFRACTION2AA182 - 306128 - 252
6X-RAY DIFFRACTION3BB55 - 651 - 11
7X-RAY DIFFRACTION3BB95 - 18141 - 127
8X-RAY DIFFRACTION3BB307 - 319253 - 265
9X-RAY DIFFRACTION4BB66 - 8512 - 31
10X-RAY DIFFRACTION4BB182 - 306128 - 252
11X-RAY DIFFRACTION5CC55 - 651 - 11
12X-RAY DIFFRACTION5CC95 - 18141 - 127
13X-RAY DIFFRACTION5CC307 - 319253 - 265
14X-RAY DIFFRACTION6CC66 - 8512 - 31
15X-RAY DIFFRACTION6CC182 - 306128 - 252
16X-RAY DIFFRACTION7DD55 - 651 - 11
17X-RAY DIFFRACTION7DD95 - 18141 - 127
18X-RAY DIFFRACTION7DD307 - 319253 - 265
19X-RAY DIFFRACTION8DD66 - 8512 - 31
20X-RAY DIFFRACTION8DD182 - 306128 - 252
21X-RAY DIFFRACTION9EE55 - 651 - 11
22X-RAY DIFFRACTION9EE95 - 18141 - 127
23X-RAY DIFFRACTION9EE307 - 319253 - 265
24X-RAY DIFFRACTION10EE66 - 8512 - 31
25X-RAY DIFFRACTION10EE182 - 306128 - 252
26X-RAY DIFFRACTION11FF55 - 651 - 11
27X-RAY DIFFRACTION11FF95 - 18141 - 127
28X-RAY DIFFRACTION11FF307 - 319253 - 265
29X-RAY DIFFRACTION12FF66 - 8512 - 31
30X-RAY DIFFRACTION12FF182 - 306128 - 252
31X-RAY DIFFRACTION13GG55 - 651 - 11
32X-RAY DIFFRACTION13GG95 - 18141 - 127
33X-RAY DIFFRACTION13GG307 - 319253 - 265
34X-RAY DIFFRACTION14GG66 - 8512 - 31
35X-RAY DIFFRACTION14GG182 - 306128 - 252
36X-RAY DIFFRACTION15HH55 - 651 - 11
37X-RAY DIFFRACTION15HH95 - 18141 - 127
38X-RAY DIFFRACTION15HH307 - 319253 - 265
39X-RAY DIFFRACTION16HH66 - 8512 - 31
40X-RAY DIFFRACTION16HH182 - 306128 - 252

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