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- PDB-10ke: Crystal structure of Capsular polysaccharide biosynthesis protein... -

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Basic information

Entry
Database: PDB / ID: 10ke
TitleCrystal structure of Capsular polysaccharide biosynthesis protein from Bordetella pertussis in complex with NAD and uridine-diphosphate-n-acetylgalactosamine (cocrystallization)
ComponentsCapsular polysaccharide biosynthesis protein
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / Capsular polysaccharide biosynthesis protein
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Capsular polysaccharide biosynthesis protein from Bordetella pertussis in complex with NAD and uridine-diphosphate-n-acetylgalactosamine (cocrystallization)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionJan 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsular polysaccharide biosynthesis protein
B: Capsular polysaccharide biosynthesis protein
C: Capsular polysaccharide biosynthesis protein
D: Capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,50916
Polymers153,2844
Non-polymers5,22512
Water18,8261045
1
A: Capsular polysaccharide biosynthesis protein
C: Capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2197
Polymers76,6422
Non-polymers2,5775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-60 kcal/mol
Surface area24110 Å2
MethodPISA
2
B: Capsular polysaccharide biosynthesis protein
D: Capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2909
Polymers76,6422
Non-polymers2,6487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-58 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.920, 155.190, 79.156
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Capsular polysaccharide biosynthesis protein / UDP-N-acetylglucosamine C4 epimerase


Mass: 38320.996 Da / Num. of mol.: 4 / Fragment: residues 9-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: wbpP, tviC, vipB, BP1630, BP3149 / Plasmid: BopeA.00085.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7TTK0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley B3: 30%(v/v) PEG 3350, 100mM Bis-Tris pH 6.5, 30 mM NaNO3, 400 mM NaCl. BopeA.00085.a.B2.PW39367 at 14.1 mg/mL. Screened as apo protein but NAD and UD2 ligands bound from the ...Details: Berkeley B3: 30%(v/v) PEG 3350, 100mM Bis-Tris pH 6.5, 30 mM NaNO3, 400 mM NaCl. BopeA.00085.a.B2.PW39367 at 14.1 mg/mL. Screened as apo protein but NAD and UD2 ligands bound from the expression host. plate 19876 well C1 drop 1, Puck: PSL-1304, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 7, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→45.4 Å / Num. obs: 140923 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.99 / Net I/σ(I): 12.6 / Num. measured all: 975749
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.953 / Num. measured all: 49317 / Num. unique obs: 6957 / CC1/2: 0.834 / Rpim(I) all: 0.382 / Rrim(I) all: 1.027 / Χ2: 1.03 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(2.0_5847: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.25 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 7327 5.21 %
Rwork0.1505 --
obs0.1523 140759 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10414 0 336 1045 11795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811155
X-RAY DIFFRACTIONf_angle_d1.01715274
X-RAY DIFFRACTIONf_dihedral_angle_d15.4164316
X-RAY DIFFRACTIONf_chiral_restr0.0561692
X-RAY DIFFRACTIONf_plane_restr0.011984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.30592200.26614464X-RAY DIFFRACTION99
1.72-1.740.26072220.24614409X-RAY DIFFRACTION97
1.74-1.760.27012270.22714401X-RAY DIFFRACTION99
1.76-1.780.22872580.20444420X-RAY DIFFRACTION98
1.78-1.810.22532630.19774377X-RAY DIFFRACTION97
1.81-1.830.26332270.19294419X-RAY DIFFRACTION99
1.83-1.860.23492470.18784352X-RAY DIFFRACTION98
1.86-1.890.25022360.18894472X-RAY DIFFRACTION99
1.89-1.910.21572230.17834448X-RAY DIFFRACTION99
1.91-1.950.22882350.18164390X-RAY DIFFRACTION98
1.95-1.980.21232290.17454482X-RAY DIFFRACTION99
1.98-2.020.22542410.16674419X-RAY DIFFRACTION98
2.02-2.050.20122220.16334419X-RAY DIFFRACTION99
2.05-2.10.20642600.15364420X-RAY DIFFRACTION99
2.1-2.140.18532870.14224412X-RAY DIFFRACTION99
2.14-2.190.18362920.13834397X-RAY DIFFRACTION99
2.19-2.250.17922350.13714471X-RAY DIFFRACTION99
2.25-2.310.19212770.14134415X-RAY DIFFRACTION100
2.31-2.380.16872880.14514412X-RAY DIFFRACTION99
2.38-2.450.18562550.14094482X-RAY DIFFRACTION99
2.45-2.540.19292310.14514471X-RAY DIFFRACTION100
2.54-2.640.19522150.14544510X-RAY DIFFRACTION99
2.64-2.760.18392260.1494461X-RAY DIFFRACTION99
2.76-2.910.18642450.15844486X-RAY DIFFRACTION99
2.91-3.090.20142630.15934453X-RAY DIFFRACTION100
3.09-3.330.16912440.15074511X-RAY DIFFRACTION100
3.33-3.660.18362190.14184518X-RAY DIFFRACTION100
3.66-4.190.14832330.12214497X-RAY DIFFRACTION99
4.19-5.280.13672440.11464530X-RAY DIFFRACTION100
5.28-44.250.16592630.15944514X-RAY DIFFRACTION99
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)
13.46790.3319-0.69451.783-1.98064.18660.0569-0.1758-0.04970.08010.21420.27840.0053-0.5877-0.2470.2059-0.019-0.02090.2537-0.00440.2191-7.9427-4.204537.8225
21.43850.34050.10341.5308-0.03940.6144-0.00160.0664-0.1435-0.1681-0.01420.06950.0756-0.01070.01270.19640.0046-0.02480.1783-0.02730.17880.0259-2.409726.7263
32.1430.29070.59991.4136-0.07141.1220.02960.01020.1191-0.1822-0.0236-0.16010.04630.0668-0.00580.1867-0.00150.00260.1445-0.0260.211911.080311.337631.144
41.91510.48950.93561.4336-0.36612.2548-0.0779-0.38630.1280.24-0.0415-0.0649-0.20990.03380.15020.24190.0167-0.01340.2446-0.06630.23169.01529.639846.9116
51.2969-1.0245-0.10682.2623-0.35380.71650.0258-0.15580.0877-0.0904-0.0318-0.1868-0.0080.15520.0110.1735-0.0038-0.01740.2432-0.01620.207213.94081.224740.1958
63.3761-0.5350.77882.6752-0.31152.752-0.0561-0.46770.02670.13210.07020.1615-0.1497-0.0158-0.00690.17790.00370.02010.2531-0.01290.15861.98260.126247.0447
73.8824-0.2494-0.24576.04372.01264.3025-0.2623-0.7697-0.82190.49560.1117-0.01020.63090.79790.11020.27510.12750.0370.49350.14960.382821.9472-17.083846.509
83.2303-1.1207-1.78670.57520.54681.6768-0.0032-0.84690.29290.13120.2012-0.357-0.03890.6184-0.19730.28970.0067-0.02790.55370.0110.413125.2638-6.150946.6974
93.8977-1.9669-1.54353.77120.98543.0947-0.051-0.278-0.62560.0513-0.05040.2580.30920.0780.10250.1783-0.0154-0.05760.22130.03250.2398.2001-11.249743.7253
102.00440.3901-0.13491.7174-0.1751.158-0.02360.0328-0.0854-0.13930.12440.19240.1263-0.1687-0.09330.1912-0.0467-0.05330.20370.03740.19723.75520.963269.4187
111.25150.0641-0.05231.8926-0.34210.8894-0.0127-0.07320.13420.05160.04770.0662-0.0121-0.046-0.03430.1543-0.0079-0.00320.16830.00370.20833.247616.306175.6612
123.4042-1.0788-0.43471.9627-0.25341.45420.039-0.31-0.13460.0169-0.0685-0.09090.04760.18980.02850.2024-0.0204-0.02050.23710.05140.194541.3163-0.506483.8788
133.51461.47830.80152.25691.47262.56050.05260.0135-0.14360.08670.2427-0.5412-0.09980.4502-0.28410.238-0.04850.02210.2683-0.05790.381431.825542.583434.9891
141.64220.20520.28031.47750.17340.8515-0.05980.25210.0862-0.35790.0978-0.2396-0.27010.1742-0.04380.2871-0.05110.0730.2351-0.02010.231823.013644.162424.217
152.99891.26610.91872.33081.38891.9895-0.13570.3516-0.2389-0.37870.1898-0.3917-0.11850.2584-0.0590.2899-0.02760.06570.2702-0.05590.317924.624628.672224.7707
162.73590.4666-0.45771.60520.12710.9849-0.02580.1615-0.1388-0.09920.0481-0.0295-0.04720.0114-0.02230.1945-0.01120.01180.1714-0.02780.231712.456326.161230.3742
171.58040.5274-0.43861.98440.69282.4013-0.0023-0.2022-0.09070.3139-0.0685-0.01380.198-0.08260.07490.22850.0068-0.01370.1870.00040.237114.522429.492745.8164
181.0394-0.6482-0.19032.59980.37490.49980.06880.0328-0.0263-0.0778-0.04630.0312-0.02140.0146-0.02010.1754-0.02430.00390.1897-0.01590.18849.295437.237538.3834
194.06-1.3126-1.36552.93120.72151.9303-0.0821-0.33630.06940.16460.17-0.43250.13030.33-0.09850.2123-0.0276-0.03280.2492-0.03010.243621.87638.426644.9599
201.9552-0.03160.76358.1452-2.55423.3813-0.0421-0.20940.43130.30070.0227-0.185-0.4491-0.18390.02970.25380.0231-0.00660.2639-0.08670.34831.255355.456943.1799
211.94790.58870.77550.40470.23940.75610.1865-0.2175-0.22230.1868-0.01270.42780.0858-0.2886-0.16880.2701-0.03150.03280.323-0.0470.3804-1.366544.401544.1138
223.1473-1.47260.88173.6175-0.87112.12850.0313-0.08410.5842-0.0741-0.0771-0.3299-0.22010.01860.0680.2236-0.04530.05580.2125-0.03490.285915.092949.683840.4229
233.78630.70690.65192.11781.19772.9113-0.0081-0.08890.12210.11260.1302-0.205-0.04130.2643-0.12210.2093-0.0077-0.00390.16040.00260.23956.46149.811874.6705
241.40750.618-0.06312.1639-0.42120.3462-0.08890.14940.0991-0.13590.05510.0957-0.0462-0.02170.03110.1944-0.0117-0.0030.16980.01120.17744.913643.062865.7114
251.79380.6325-0.47481.72740.37342.2727-0.0567-0.2741-0.06650.3328-0.09220.16720.1651-0.15330.14720.2370.01410.01920.18840.00610.233439.734736.428385.0334
261.1492-0.6404-0.1422.62670.36720.3970.0311-0.07090.064-0.0023-0.08950.27630.0102-0.06620.05560.1743-0.01560.0070.1948-0.02080.238634.51544.218277.877
273.2255-0.2627-0.8172.40320.20912.26020.062-0.35050.16610.1367-0.0218-0.14380.00040.066-0.04210.1973-0.0172-0.02210.2214-0.0240.174546.769345.526984.424
282.9595-0.7931.55340.8581-0.49722.1903-0.025-0.51770.07240.14350.05480.48560.1027-0.6374-0.00550.2361-0.02910.0250.3933-0.12870.467324.3656.016683.7657
293.8386-1.46031.0613.2441-0.49182.2316-0.1088-0.22760.75930.1757-0.04850.0035-0.2277-0.16260.18550.1877-0.03530.03450.1915-0.03570.360540.120856.61880.6994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 97 )
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 238 )
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 270 )
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 285 )
8X-RAY DIFFRACTION8chain 'A' and (resid 286 through 310 )
9X-RAY DIFFRACTION9chain 'A' and (resid 311 through 341 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 209 )
12X-RAY DIFFRACTION12chain 'B' and (resid 210 through 341 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 76 )
15X-RAY DIFFRACTION15chain 'C' and (resid 77 through 97 )
16X-RAY DIFFRACTION16chain 'C' and (resid 98 through 131 )
17X-RAY DIFFRACTION17chain 'C' and (resid 132 through 164 )
18X-RAY DIFFRACTION18chain 'C' and (resid 165 through 238 )
19X-RAY DIFFRACTION19chain 'C' and (resid 239 through 270 )
20X-RAY DIFFRACTION20chain 'C' and (resid 271 through 285 )
21X-RAY DIFFRACTION21chain 'C' and (resid 286 through 310 )
22X-RAY DIFFRACTION22chain 'C' and (resid 311 through 341 )
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 26 )
24X-RAY DIFFRACTION24chain 'D' and (resid 27 through 131 )
25X-RAY DIFFRACTION25chain 'D' and (resid 132 through 164 )
26X-RAY DIFFRACTION26chain 'D' and (resid 165 through 238 )
27X-RAY DIFFRACTION27chain 'D' and (resid 239 through 270 )
28X-RAY DIFFRACTION28chain 'D' and (resid 271 through 310 )
29X-RAY DIFFRACTION29chain 'D' and (resid 311 through 341 )

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