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- PDB-8iq9: Crystal structure of trimeric K2-2 TSP in complex with tetrasacch... -

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Basic information

Entry
Database: PDB / ID: 8iq9
TitleCrystal structure of trimeric K2-2 TSP in complex with tetrasaccharide and octasaccharide
ComponentsK2-2 TSP
KeywordsHYDROLASE / bacteriophage / tailspike protein / Klebsiella pneumoniae K2
Function / homologyACETYL GROUP
Function and homology information
Biological speciesKlebsiella phage VLC6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsYe, T.J. / Ko, T.P. / Huang, K.F. / Wu, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Mbio / Year: 2024
Title: Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation.
Authors: Ye, T.J. / Fung, K.M. / Lee, I.M. / Ko, T.P. / Lin, C.Y. / Wong, C.L. / Tu, I.F. / Huang, T.Y. / Yang, F.L. / Chang, Y.P. / Wang, J.T. / Lin, T.L. / Huang, K.F. / Wu, S.H.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K2-2 TSP
B: K2-2 TSP
C: K2-2 TSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,37628
Polymers194,4433
Non-polymers5,93325
Water40,3542240
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.405, 86.357, 103.420
Angle α, β, γ (deg.)90.000, 110.212, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 83 or resid 85...
d_2ens_1(chain "B" and (resid 15 through 83 or resid 85...
d_3ens_1(chain "C" and (resid 15 through 83 or resid 85...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUGLYGLYAA15 - 8346 - 114
d_12ILEILESERSERAA85 - 96116 - 127
d_13ILEILEALAALAAA98 - 123129 - 154
d_14TYRTYRPHEPHEAA125 - 127156 - 158
d_15GLYGLYSERSERAA129 - 159160 - 190
d_16VALVALTYRTYRAA161 - 168192 - 199
d_17TYRTYRLEULEUAA170 - 183201 - 214
d_18GLYGLYARGARGAA185 - 231216 - 262
d_19GLYGLYLEULEUAA233 - 269264 - 300
d_110PHEPHEPHEPHEAA271 - 295302 - 326
d_111THRTHRCYSCYSAA297 - 317328 - 348
d_112GLYGLYASNASNAA319 - 354350 - 385
d_113ASNASNSERSERAA356 - 367387 - 398
d_114ASPASPGLUGLUAA369 - 388400 - 419
d_115GLUGLULEULEUAA390 - 412421 - 443
d_116ASNASNPROPROAA414 - 472445 - 503
d_117SERSERSERSERAA474 - 494505 - 525
d_118METMETLYSLYSAA496 - 577527 - 608
d_119BGCBGCBGCBGCDD1
d_120GLCGLCGLCGLCDD2
d_21GLUGLUGLYGLYBB15 - 8346 - 114
d_22ILEILESERSERBB85 - 96116 - 127
d_23ILEILEALAALABB98 - 123129 - 154
d_24TYRTYRPHEPHEBB125 - 127156 - 158
d_25GLYGLYSERSERBB129 - 159160 - 190
d_26VALVALTYRTYRBB161 - 168192 - 199
d_27TYRTYRLEULEUBB170 - 183201 - 214
d_28GLYGLYARGARGBB185 - 231216 - 262
d_29GLYGLYLEULEUBB233 - 269264 - 300
d_210PHEPHEPHEPHEBB271 - 295302 - 326
d_211THRTHRCYSCYSBB297 - 317328 - 348
d_212GLYGLYASNASNBB319 - 354350 - 385
d_213ASNASNSERSERBB356 - 367387 - 398
d_214ASPASPGLUGLUBB369 - 388400 - 419
d_215GLUGLULEULEUBB390 - 412421 - 443
d_216ASNASNPROPROBB414 - 472445 - 503
d_217SERSERSERSERBB474 - 494505 - 525
d_218METMETLYSLYSBB496 - 577527 - 608
d_219BGCBGCBGCBGCFF1
d_220GLCGLCGLCGLCFF2
d_31GLUGLUGLYGLYCC15 - 8346 - 114
d_32ILEILESERSERCC85 - 96116 - 127
d_33ILEILEALAALACC98 - 123129 - 154
d_34TYRTYRPHEPHECC125 - 127156 - 158
d_35GLYGLYSERSERCC129 - 159160 - 190
d_36VALVALTYRTYRCC161 - 168192 - 199
d_37TYRTYRLEULEUCC170 - 183201 - 214
d_38GLYGLYARGARGCC185 - 231216 - 262
d_39GLYGLYLEULEUCC233 - 269264 - 300
d_310PHEPHEPHEPHECC271 - 295302 - 326
d_311THRTHRCYSCYSCC297 - 317328 - 348
d_312GLYGLYASNASNCC319 - 354350 - 385
d_313ASNASNSERSERCC356 - 367387 - 398
d_314ASPASPGLUGLUCC369 - 388400 - 419
d_315GLUGLULEULEUCC390 - 412421 - 443
d_316ASNASNPROPROCC414 - 472445 - 503
d_317SERSERSERSERCC474 - 494505 - 525
d_318METMETLYSLYSCC496 - 577527 - 608
d_319BGCBGCBGCBGCHH1
d_320GLCGLCGLCGLCHH2

NCS oper:
IDCodeMatrixVector
1given(0.679114078407, 0.39529662038, -0.618501940519), (-0.410496377439, -0.494006171969, -0.766453277223), (-0.608520166157, 0.774402017025, -0.173218715524)28.5310169932, 17.3294552743, 54.757640645
2given(0.686953385717, -0.408209643584, -0.601215379658), (0.379218624586, -0.504376061825, 0.775756419906), (-0.619909897178, -0.7609005685, -0.191682143763)20.5090216895, -44.3655364964, 40.7518187317

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein K2-2 TSP


Mass: 64814.355 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage VLC6 (virus) / Gene: VLC6_58 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 2 types, 5 molecules

#2: Polysaccharide alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D- ...alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-[alpha-D-glucopyranuronic acid-(1-3)]beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1343.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAa1-3DManpb1-4DGlcpa1-3DGlcpb1-4[DGlcpAa1-3]DManpb1-4DGlcpa1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5][a2122h-1a_1-5][a1122h-1b_1-5][a2122A-1a_1-5]/1-2-3-4-1-2-3-4/a3-b1_b4-c1_c3-d1_c4-e1_e3-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-GlcpA]{}[(4+1)][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-GlcpA]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D- ...alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 680.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAa1-3DManpb1-4DGlcpa1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2122h-1a_1-5][a1122h-1b_1-5][a2122A-1a_1-5]/1-2-3-4/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(4+1)][b-D-Manp]{[(3+1)][a-D-GlcpA]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 2260 molecules

#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine pH 9.0, 22 % PEG-6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 230579 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.57 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Rsym value: 0.034 / Χ2: 1.391 / Net I/σ(I): 26.6
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.579 / Num. unique obs: 22985 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.348 / Rrim(I) all: 0.677 / Rsym value: 0.49 / Χ2: 1.105 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IQ5

8iq5


Resolution: 1.58→26.95 Å / SU ML: 0.1362 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1729 2000 0.87 %
Rwork0.1434 228557 -
obs0.1436 230557 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.98 Å2
Refinement stepCycle: LAST / Resolution: 1.58→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12558 0 398 2240 15196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713300
X-RAY DIFFRACTIONf_angle_d1.034918066
X-RAY DIFFRACTIONf_chiral_restr0.07162124
X-RAY DIFFRACTIONf_plane_restr0.0092301
X-RAY DIFFRACTIONf_dihedral_angle_d11.94824674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.712955558752
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.05962349061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.22181400.2116057X-RAY DIFFRACTION98.49
1.62-1.660.23831430.197716329X-RAY DIFFRACTION99.98
1.66-1.710.23321420.185916206X-RAY DIFFRACTION100
1.71-1.770.19151430.175316317X-RAY DIFFRACTION99.99
1.77-1.830.18741420.160216284X-RAY DIFFRACTION99.99
1.83-1.90.19781420.151216270X-RAY DIFFRACTION99.99
1.9-1.990.2041440.148816384X-RAY DIFFRACTION99.98
1.99-2.090.1561430.144316284X-RAY DIFFRACTION99.94
2.09-2.230.18261420.137616275X-RAY DIFFRACTION99.97
2.23-2.40.181430.139116387X-RAY DIFFRACTION99.98
2.4-2.640.18951430.14216337X-RAY DIFFRACTION99.99
2.64-3.020.1751430.142516349X-RAY DIFFRACTION99.9
3.02-3.80.13731440.127216468X-RAY DIFFRACTION99.93
3.8-26.950.15391460.13116610X-RAY DIFFRACTION99.82
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)
10.0475311427493-0.0943812415122-0.07237405991220.3948389820660.1775494649980.183242844983-0.00774088055011-0.0851895670140.08680342748060.07893173253040.0470565989643-0.426272098370.02963078772840.2395204089820.01637707128810.1893075470730.01289887337730.03432399009960.1399113842420.01298655137380.19620889389863.3248040799-11.2174971513-6.19536897122
20.549819088702-0.112581393405-0.2505593019230.2381132512050.06528740101040.305008070010.01284083231730.01725659348720.0455210033701-0.0515543669196-0.007065002844150.01445051415-0.00451259473391-0.0282879521813-8.31198870982E-60.121367457551-0.00128133512009-0.02221383729850.08565032666110.004529874363240.096975196105125.2239897076-3.5008527422210.8249236056
30.44059886448-0.00245442890786-0.01279314897710.449526829270.1553799879080.2221778103610.0268885268076-0.0869522141187-0.05748683034060.0475794826214-0.03954819254210.161604288272-0.046560286214-0.0752118768373-2.00620578688E-50.1551454186990.02426415012720.0267299513930.214437116207-0.01683214728230.238007735261-12.899596889312.304024461837.5905937771
40.1757349654380.08528911485960.04679313310290.04625459723590.06172602916770.2464029742010.0571312000275-0.0722626810064-0.1242445740570.0532769599178-0.05571255455740.1023484640960.0321407593583-0.0180683557836-4.78678133528E-60.1507867625840.01715277690940.02398344057310.193230149469-0.01792991891880.196406566844-5.6616143920410.828042620738.4033712686
50.08158163930320.0006482413757610.006981479823570.223230629669-0.1461531226470.125050038151-0.03328294292690.229144733737-0.116112102922-0.331526578303-0.0813085472569-0.1786946043590.1681065235520.241715268593-0.002834503304370.192215768256-0.007732679685780.01518544421840.2261494742580.04456436369020.2033916931371.13298500171.803391320228.81545127909
60.5739218556510.123867762518-0.2511749302980.296994484014-0.1018832618850.3352651735680.0255998962928-0.1742358069670.07200531372650.0477979914388-0.0456077420182-0.0121718636953-0.03400456809340.07991897013350.0004227611801610.118403521153-0.0159058925817-0.02330404530930.147631897682-0.02433920266360.0850311220937.51902901670.40166018125434.6399268247
70.616753949221-0.6210299116890.2260345659461.16824989664-0.01613218058570.4950991006240.555702415136-0.8390655961760.1047135624710.906639326233-0.3003019337341.292872577280.0553493742809-0.2992413185960.4306137835160.442637286699-0.2211837149560.4963628642630.74375039593-0.2891694975780.5697234290572.70849004141-13.247034324764.4882195632
80.04751489802240.01081619791250.04716015451350.01249787007430.04885021940610.121977177402-0.03215527915930.1300141799550.0331097263876-0.1671060813790.00755236074673-0.305077525454-0.177586546090.2913775913020.0001570536309580.1827474298420.02140518556220.0134000540860.2287891594910.02077906127640.27668975532172.2245363645-19.365922232811.4618486474
90.5797962352010.0276064198804-0.2200715414120.290483863264-0.001502954501740.265041898624-0.0440846085995-0.0997993076209-0.1111449171770.00164913028794-0.0159819753557-0.03710513766520.08041784805280.0582924683081-0.0007267833404140.1464568378590.0133470235883-0.001506311317350.1146885442120.03531733164910.10550886698536.671742762-24.839090852725.5364393797
100.0813943892012-0.0363785993969-0.0304838151470.045851018543-0.01533716708710.0648695939649-0.0429687314539-0.00115883506851-0.136802825508-0.0120322981237-0.02105282467920.1804294215530.044482907374-0.159437355024-4.46166060176E-50.164000870112-0.03022084549410.001826564709890.190591796085-0.00188313148190.2246074372430.72841880569-23.548163044827.8988815678
110.205258800456-0.0473749623982-0.1235783544040.1364797649880.02526216798180.265053295938-0.0203279147128-0.079219630634-0.21378819601-0.0680834120124-0.03061109672620.4121318336930.0250090317311-0.103261106789-0.001017309067310.214365225778-0.0483167016640.01950721082470.27081390046-0.01403582895450.505468931632-16.0703532209-26.362783745132.2015237046
120.114864202692-0.0689678473889-0.0335589480440.152122332796-0.133510356780.166646198417-0.0280061167776-0.0478135484456-0.111414045587-0.0116853557082-0.02304572036520.405324267676-0.0253793885936-0.1568318415012.16099156617E-50.209624123903-0.04004452551140.01013618693390.266423113264-0.01996104533430.33891638213-11.2751547568-22.352021545828.7591012367
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 50 )AA15 - 501 - 36
22chain 'A' and (resid 51 through 430 )AA51 - 43037 - 416
33chain 'A' and (resid 431 through 533 )AA431 - 533417 - 519
44chain 'A' and (resid 534 through 579 )AA534 - 579520 - 565
55chain 'B' and (resid 15 through 50 )BB15 - 501 - 36
66chain 'B' and (resid 51 through 430 )BB51 - 43037 - 416
77chain 'B' and (resid 431 through 577 )BB431 - 577417 - 563
88chain 'C' and (resid 15 through 50 )CC15 - 501 - 36
99chain 'C' and (resid 51 through 386 )CC51 - 38637 - 372
1010chain 'C' and (resid 387 through 430 )CC387 - 430373 - 416
1111chain 'C' and (resid 431 through 533 )CC431 - 533417 - 519
1212chain 'C' and (resid 534 through 579 )CC534 - 579520 - 565

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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