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- PDB-9pmn: Crystal structure of Capsular polysaccharide biosynthesis protein... -

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Basic information

Entry
Database: PDB / ID: 9pmn
TitleCrystal structure of Capsular polysaccharide biosynthesis protein from Bordetella pertussis in complex with NAD and uridine-diphosphate-n-acetylgalactosamine
ComponentsCapsular polysaccharide biosynthesis protein
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Capsular polysaccharide biosynthesis protein / Bordetella pertussis
Function / homology: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / ACETATE ION / 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: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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
Authors: Enayati, P. / Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: 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)158,97025
Polymers153,2844
Non-polymers5,68621
Water5,783321
1
A: Capsular polysaccharide biosynthesis protein
C: Capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,52613
Polymers76,6422
Non-polymers2,88411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-62 kcal/mol
Surface area24710 Å2
MethodPISA
2
B: Capsular polysaccharide biosynthesis protein
D: Capsular polysaccharide biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,44312
Polymers76,6422
Non-polymers2,80110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-71 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.726, 155.942, 79.958
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 38320.996 Da / Num. of mol.: 4 / Fragment: T2-R348
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

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Non-polymers , 5 types, 342 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / 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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus C1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4. BopeA.00085.a.B2.PW39367 at 14.1 mg/mL. Screened as apo ...Details: Morpheus C1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4. 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-1013, 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: Jun 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: 2.4→44.19 Å / Num. obs: 51167 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.073 / Rrim(I) all: 0.17 / Χ2: 0.99 / Net I/σ(I): 6.9 / Num. measured all: 268542
Reflection shellResolution: 2.4→2.47 Å / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.981 / Num. measured all: 22259 / Num. unique obs: 4434 / CC1/2: 0.733 / Rpim(I) all: 0.484 / Rrim(I) all: 1.098 / Χ2: 1.03 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX2.0_5750refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.19 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 2592 5.08 %
Rwork0.1929 --
obs0.1956 51005 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10432 0 363 321 11116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211042
X-RAY DIFFRACTIONf_angle_d0.60415084
X-RAY DIFFRACTIONf_dihedral_angle_d14.1984224
X-RAY DIFFRACTIONf_chiral_restr0.0411669
X-RAY DIFFRACTIONf_plane_restr0.0051958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.33821470.29712551X-RAY DIFFRACTION99
2.44-2.490.3221280.26982533X-RAY DIFFRACTION100
2.49-2.540.32771670.2562529X-RAY DIFFRACTION100
2.54-2.60.29241460.26092524X-RAY DIFFRACTION99
2.6-2.660.35811320.25682540X-RAY DIFFRACTION99
2.66-2.720.3211310.24732512X-RAY DIFFRACTION100
2.72-2.80.29161500.23472560X-RAY DIFFRACTION100
2.8-2.880.33161560.22992508X-RAY DIFFRACTION100
2.88-2.970.31991400.2352567X-RAY DIFFRACTION100
2.97-3.080.25441400.21882520X-RAY DIFFRACTION100
3.08-3.20.27651350.2052566X-RAY DIFFRACTION100
3.2-3.350.25741350.19772563X-RAY DIFFRACTION100
3.35-3.520.27341290.20082546X-RAY DIFFRACTION100
3.52-3.740.20571120.17282566X-RAY DIFFRACTION100
3.74-4.030.19611250.15622561X-RAY DIFFRACTION100
4.03-4.440.18081270.13982580X-RAY DIFFRACTION99
4.44-5.080.18911480.14782517X-RAY DIFFRACTION99
5.08-6.40.21361190.17212570X-RAY DIFFRACTION99
6.4-44.190.22461250.17952600X-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)
15.28580.9329-1.70044.0066-0.13713.7249-0.03270.0840.00770.15750.0870.17690.2518-0.184-0.0120.3368-0.025-0.06190.268-0.00150.2688-30.2736-5.1659-2.6655
22.50840.32980.27212.73920.43661.2553-0.02510.01190.0156-0.0840.0396-0.26710.0320.034800.35310.0025-0.05150.2681-0.01120.3014-21.29063.5511-11.8306
32.02090.10430.93492.5653-0.59850.8641-0.1172-0.13240.1876-0.0195-0.0096-0.157-0.1229-0.00180.14540.3727-0.0034-0.00620.3464-0.01070.3746-16.4738.6673.0633
46.5204-0.3759-0.42973.3412-0.06521.39340.0586-0.54490.3150.2265-0.1218-0.63250.09640.21090.02090.3761-0.0003-0.09430.44680.08550.5215-1.4569-8.44313.253
53.08330.5953.61973.1598-0.47745.5058-0.1622-0.5495-0.1750.1153-0.01980.2322-0.2583-0.35430.11920.4448-0.00110.02810.4006-0.02560.327-23.20760.47177.7729
67.95753.39542.09834.31145.6658.5973-0.0139-0.9186-0.84951.3283-0.0983-0.53310.8390.35580.06550.4820.0741-0.05010.43450.10040.5212-3.0378-16.42437.2065
75.76111.0914-1.97340.6651-0.48341.0310.4752-0.58790.34680.1506-0.1538-0.6566-0.28990.2015-0.33560.5711-0.0083-0.12480.49040.04580.42960.1561-5.50927.7664
87.6928-6.4727-5.43646.97614.60467.1946-0.4132-0.6115-0.57830.17780.29210.25220.1560.64520.14420.3395-0.0812-0.09970.3540.02420.4273-16.8755-10.77574.3257
91.21290.9304-0.18263.1932-0.68271.23790.02770.10640.0055-0.40570.12160.38320.2333-0.2313-0.13780.359-0.0192-0.0780.36360.01590.35380.89449.045630.3878
102.99130.56110.2561.8616-0.83181.93520.0115-0.25340.19250.3176-0.03920.1382-0.0766-0.00670.04780.366-0.01940.00610.2634-0.02630.3967.327620.791644.7389
113.4672-1.5884-0.7334.6101-0.27281.39220.00120.12610.2292-0.1934-0.0866-0.3612-0.09190.15270.11470.2824-0.023-0.04210.31080.02350.347217.24163.561540.8304
122.5924-2.38162.57346.5363-1.03783.49390.14160.0929-0.25590.01360.01260.7907-0.1769-0.1032-0.16210.3256-0.04070.01740.33160.02240.29941.68458.280147.1432
133.58441.9718-0.28638.16587.28818.3708-0.3288-0.4488-0.56030.67250.2558-0.03811.02080.4450.02710.39670.1264-0.01740.56740.13980.626421.8338-8.220346.868
144.5869-1.5674-1.73392.42220.06781.78360.0571-0.0431-0.11270.0598-0.2663-0.0838-0.01070.0660.19330.3072-0.0371-0.02170.25030.05630.28915.3943-0.176545.4616
153.98092.26081.91293.04692.29934.9888-0.1409-0.1212-0.4636-0.17830.403-1.369-0.42590.6243-0.12710.4179-0.02580.03560.4522-0.12430.89536.020843.0225-4.3272
162.2971-0.2993-0.37262.9571-0.24422.6220.02890.12760.4235-0.93510.0416-0.948-0.48060.3155-0.03880.6917-0.06810.17310.4109-0.02650.7239-2.952144.6872-14.9867
173.38710.98580.38483.90650.93742.36410.0958-0.0734-0.0327-0.12910.0572-0.34540.03570.1028-0.13880.42340.0293-0.01880.289-0.0280.5115-9.027128.5944-4.2615
180.9003-0.4953-0.39745.22980.27920.14820.0218-0.0495-0.035-0.0042-0.0108-0.1197-0.0812-0.0319-0.00840.41680.0218-0.05010.4385-0.09390.5373-12.762934.83-1.8846
197.3568-3.92371.51154.5964-0.4281.83690.1094-0.3075-0.40110.23560.00430.4713-0.0244-0.2413-0.0480.4744-0.05620.00340.3841-0.09410.5716-16.967545.09542.2048
204.6021-2.5276-0.22876.95390.63262.4035-0.3531-0.40230.12050.47820.3018-0.23990.1705-0.1640.11330.4773-0.0788-0.01980.4318-0.11130.4503-13.390745.80716.421
215.7415-1.48461.97343.8139-1.72381.67190.1243-0.374-0.58860.67510.13131.03520.1563-0.3513-0.26940.7008-0.0201-0.00740.542-0.20670.7317-26.884645.454.9544
226.4521-3.05874.35984.5956-2.08426.0354-0.333-0.11150.90780.29880.0419-0.5467-0.54440.07690.24260.42760.0089-0.03890.4283-0.14610.6857-10.332650.47691.12
239.01653.55773.41056.39633.71543.0671-0.16660.49760.46460.12380.3556-0.09480.11180.4125-0.18450.274-0.02230.00170.27490.06140.355730.540651.173335.7684
242.06630.8245-0.8843.7313-0.58420.7071-0.04460.16410.0724-0.34780.09160.13580.0332-0.1015-0.05920.3087-0.0004-0.01230.29460.02050.278419.106144.024326.9485
252.0252-0.2786-0.06152.9798-0.00721.87070.0107-0.01390.00790.1355-0.0368-0.04690.02110.03780.03030.2896-0.0111-0.00630.2306-0.02040.333714.944334.887843.9759
263.7479-2.89290.88124.1902-0.72491.5312-0.0654-0.2617-0.05860.04560.06040.43830.0138-0.21580.03870.2649-0.033-0.03140.2725-0.0330.41228.201551.456739.2287
274.0714-1.50080.06824.9401-0.81653.7687-0.5218-0.61170.30360.76170.3278-0.0065-0.0202-0.28140.18920.2733-0.0479-0.00390.263-0.11440.229411.149153.722146.3108
284.6943-1.55072.56644.4795-2.82672.80340.0323-0.6345-0.48550.16080.51381.08710.2869-0.7361-0.52730.5192-0.03460.03480.5136-0.09720.6149-2.527352.965845.1046
295.6405-1.86143.96116.7691-3.02947.013-0.33590.03210.89840.03270.057-0.1381-0.5489-0.10820.37550.2024-0.02140.10040.2763-0.00250.418613.853158.637940.8735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 238 )
5X-RAY DIFFRACTION5chain 'A' and (resid 239 through 270 )
6X-RAY DIFFRACTION6chain 'A' and (resid 271 through 285 )
7X-RAY DIFFRACTION7chain 'A' and (resid 286 through 310 )
8X-RAY DIFFRACTION8chain 'A' and (resid 311 through 341 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 132 )
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 184 )
11X-RAY DIFFRACTION11chain 'B' and (resid 185 through 238 )
12X-RAY DIFFRACTION12chain 'B' and (resid 239 through 270 )
13X-RAY DIFFRACTION13chain 'B' and (resid 271 through 285 )
14X-RAY DIFFRACTION14chain 'B' and (resid 286 through 341 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 26 )
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 77 through 164 )
18X-RAY DIFFRACTION18chain 'C' and (resid 165 through 219 )
19X-RAY DIFFRACTION19chain 'C' and (resid 220 through 250 )
20X-RAY DIFFRACTION20chain 'C' and (resid 251 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 132 )
25X-RAY DIFFRACTION25chain 'D' and (resid 133 through 184 )
26X-RAY DIFFRACTION26chain 'D' and (resid 185 through 250 )
27X-RAY DIFFRACTION27chain 'D' and (resid 251 through 285 )
28X-RAY DIFFRACTION28chain 'D' and (resid 286 through 310 )
29X-RAY DIFFRACTION29chain 'D' and (resid 311 through 341 )

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