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- PDB-9fve: Crystal structure of VcSiaP W73A mutant in complex with sialic ac... -

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Basic information

Entry
Database: PDB / ID: 9fve
TitleCrystal structure of VcSiaP W73A mutant in complex with sialic acid and a VHH antibody (VHH_VcP#2)
Components
  • Sialic acid-binding periplasmic protein SiaP
  • VHH_VcP#2
KeywordsTRANSPORT PROTEIN / Substrate binding protein / sialic acid / TRAP transporter / VHH antibody / Nanobody / Complex
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / N-acetyl-beta-neuraminic acid / Sialic acid-binding periplasmic protein SiaP
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSchneberger, N. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Commun Biol / Year: 2024
Title: Allosteric substrate release by a sialic acid TRAP transporter substrate binding protein.
Authors: Schneberger, N. / Hendricks, P. / Peter, M.F. / Gehrke, E. / Binder, S.C. / Koenig, P.A. / Menzel, S. / Thomas, G.H. / Hagelueken, G.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-binding periplasmic protein SiaP
B: VHH_VcP#2
C: Sialic acid-binding periplasmic protein SiaP
D: VHH_VcP#2
E: Sialic acid-binding periplasmic protein SiaP
F: VHH_VcP#2
G: Sialic acid-binding periplasmic protein SiaP
H: VHH_VcP#2
I: Sialic acid-binding periplasmic protein SiaP
J: VHH_VcP#2
K: Sialic acid-binding periplasmic protein SiaP
L: VHH_VcP#2
M: Sialic acid-binding periplasmic protein SiaP
N: VHH_VcP#2
O: Sialic acid-binding periplasmic protein SiaP
P: VHH_VcP#2
Q: Sialic acid-binding periplasmic protein SiaP
R: VHH_VcP#2
T: VHH_VcP#2
U: Sialic acid-binding periplasmic protein SiaP
V: VHH_VcP#2
W: Sialic acid-binding periplasmic protein SiaP
X: VHH_VcP#2
Y: Sialic acid-binding periplasmic protein SiaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,96942
Polymers569,70624
Non-polymers4,26418
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.570, 153.113, 210.487
Angle α, β, γ (deg.)90.000, 89.999, 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_1chain "A"
d_2ens_1chain "C"
d_3ens_1(chain "E" and (resid 1 through 299 or resid 301))
d_4ens_1(chain "G" and (resid 1 through 299 or resid 301))
d_5ens_1chain "I"
d_6ens_1chain "K"
d_7ens_1chain "M"
d_8ens_1chain "O"
d_9ens_1(chain "Q" and (resid 1 through 299 or resid 301))
d_10ens_1(chain "U" and (resid 1 through 299 or resid 301))
d_11ens_1chain "W"
d_12ens_1chain "Y"
d_1ens_2(chain "B" and resid 1 through 121)
d_2ens_2chain "D"
d_3ens_2(chain "F" and resid 1 through 121)
d_4ens_2(chain "H" and resid 1 through 121)
d_5ens_2(chain "J" and resid 1 through 121)
d_6ens_2(chain "L" and resid 1 through 121)
d_7ens_2(chain "N" and resid 1 through 121)
d_8ens_2(chain "P" and resid 1 through 121)
d_9ens_2(chain "R" and resid 1 through 121)
d_10ens_2(chain "T" and resid 1 through 121)
d_11ens_2(chain "V" and resid 1 through 121)
d_12ens_2(chain "X" and resid 1 through 121)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAMETMETAA1 - 2995 - 303
d_12ens_1SLBSLBSLBSLBAY301
d_21ens_1ALAALAMETMETCC1 - 2995 - 303
d_22ens_1SLBSLBSLBSLBCZ301
d_31ens_1ALAALAMETMETEE1 - 2995 - 303
d_32ens_1SLBSLBSLBSLBEAA301
d_41ens_1ALAALAMETMETGG1 - 2995 - 303
d_42ens_1SLBSLBSLBSLBGCA301
d_51ens_1ALAALAMETMETII1 - 2995 - 303
d_52ens_1SLBSLBSLBSLBIEA301
d_61ens_1ALAALAMETMETKK1 - 2995 - 303
d_62ens_1SLBSLBSLBSLBKFA301
d_71ens_1ALAALAMETMETMM1 - 2995 - 303
d_72ens_1SLBSLBSLBSLBMGA301
d_81ens_1ALAALAMETMETOO1 - 2995 - 303
d_82ens_1SLBSLBSLBSLBOHA301
d_91ens_1ALAALAMETMETQQ1 - 2995 - 303
d_92ens_1SLBSLBSLBSLBQIA301
d_101ens_1ALAALAMETMETUT1 - 2995 - 303
d_102ens_1SLBSLBSLBSLBUKA301
d_111ens_1ALAALAMETMETWV1 - 2995 - 303
d_112ens_1SLBSLBSLBSLBWOA301
d_121ens_1ALAALAMETMETYX1 - 2995 - 303
d_122ens_1SLBSLBSLBSLBYPA301
d_11ens_2GLNGLNSERSERBB1 - 1213 - 123
d_21ens_2GLNGLNSERSERDD1 - 1213 - 123
d_31ens_2GLNGLNSERSERFF1 - 1213 - 123
d_41ens_2GLNGLNSERSERHH1 - 1213 - 123
d_51ens_2GLNGLNSERSERJJ1 - 1213 - 123
d_61ens_2GLNGLNSERSERLL1 - 1213 - 123
d_71ens_2GLNGLNSERSERNN1 - 1213 - 123
d_81ens_2GLNGLNSERSERPP1 - 1213 - 123
d_91ens_2GLNGLNSERSERRR1 - 1213 - 123
d_101ens_2GLNGLNSERSERTS1 - 1213 - 123
d_111ens_2GLNGLNSERSERVU1 - 1213 - 123
d_121ens_2GLNGLNSERSERXW1 - 1213 - 123

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.521827736085, 0.738052128245, 0.427755619303), (-0.672434135335, -0.0473362634279, -0.738641734403), (-0.524907751408, -0.673081224042, 0.520992819868)-161.160166355, -3.10197195984, -61.86872198
2given(0.534726382151, -0.763743128774, -0.361613231896), (-0.575586694352, -0.0158840061525, -0.817586482051), (0.618682191045, 0.645324826424, -0.448093979969)44.6407702492, 13.1110787316, 171.768347095
3given(-0.457440473545, -0.743925284769, -0.487158479187), (0.772520918805, -0.0611336457037, -0.632039640664), (0.440408495799, -0.66546062847, 0.602662848353)-112.044027007, 147.602318912, -10.7881216061
4given(0.451181384715, 0.718765253495, 0.528972464742), (0.787365881509, -0.0415756655392, -0.615082460058), (-0.42010751805, 0.694008627038, -0.584689403764)-3.80498859838, 155.4884459, 119.02634059
5given(0.344225371635, -0.650821759893, 0.67671259067), (-0.849483854035, 0.0910703520089, 0.519695461515), (-0.399857568713, -0.753748782974, -0.521513851119)-137.836053059, -159.762873653, 3.72791714239
6given(-0.38890304771, 0.68216574952, -0.619196503271), (-0.790549669792, 0.0980107805172, 0.604504016938), (0.473059868382, 0.724599045738, 0.501169216775)18.4967114834, -156.279650732, 109.495534175
7given(0.624137229416, 0.636957906919, -0.452479108546), (0.55543796238, 0.0455723020779, 0.830308277226), (0.549491936978, -0.76955038178, -0.325347231583)64.7759354465, -19.5349125527, 150.021770533
8given(-0.611235248591, -0.630259865722, 0.478710739947), (0.592623537173, 0.0364367275358, 0.804655024265), (-0.524584420346, 0.775528765777, 0.351235418749)-175.891915076, -20.6187183376, -43.6901125996
9given(0.12947054626, -0.104100993631, -0.98610362578), (-0.0502891390479, -0.993883425546, 0.098319575463), (-0.990307215032, 0.0368608132092, -0.133913779368)5.36406178454, -98.6849749092, -100.867226965
10given(-0.980208657746, 0.0308004177553, -0.195556440817), (0.059305377502, 0.988141737922, -0.141629015302), (0.188875248454, -0.150423535533, -0.970411716994)-97.8548383725, 14.5983419265, 118.559625964
11given(-0.151254824068, 0.0518041345648, 0.987136419062), (-0.0449298256288, -0.997954009563, 0.0454874220654), (0.987473183922, -0.0374716751585, 0.153272908877)-121.515563287, -88.6167304965, 204.334952543
12given(-0.512854346547, 0.716100517507, 0.473476998443), (-0.707760213644, -0.0405534487103, -0.705287812017), (-0.485855842005, -0.696818101533, 0.5276254677)-164.426648423, -9.41124003205, -59.006266233
13given(0.47569339053, -0.796379568087, -0.373490805429), (-0.599094773171, 0.0175651453528, -0.800485426743), (0.644050658695, 0.604542016077, -0.468751213153)38.2066180375, 10.0130851875, 174.880039475
14given(-0.477294507595, -0.749558972036, -0.458640709554), (0.748204878746, -0.07292912576, -0.659447345917), (0.460846408732, -0.657907812734, 0.595632350954)-116.607846216, 146.692906589, -7.56455976804
15given(0.475863821304, 0.715394689054, 0.511628832697), (0.754965847441, -0.0338271847772, -0.654891052594), (-0.451198617874, 0.697901254077, -0.556195691089)0.43312837566, 155.41167036, 113.415171137
16given(0.3947472075, -0.657052125074, 0.642228267134), (-0.801499702437, 0.0954764668014, 0.59032403922), (-0.449191350278, -0.747774531007, -0.488938014081)-129.687523498, -159.892741595, -4.20031325899
17given(-0.377795730246, 0.699514234016, -0.606589006343), (-0.760018973267, 0.139883921021, 0.634668140775), (0.528811447004, 0.700794067504, 0.478796541831)19.0484926347, -154.075137911, 116.659279055
18given(0.593185284416, 0.635144640178, -0.494694354532), (0.614988668953, 0.0390515617557, 0.787568354229), (0.519538406099, -0.771405380832, -0.367441945089)64.7269699703, -9.49516200846, 150.098750981
19given(-0.577696564947, -0.62594738706, 0.523886006189), (0.643857117035, 0.045051192728, 0.763818304885), (-0.501711761564, 0.778562944576, 0.376994760762)-175.619068738, -11.305068748, -43.2018369107
20given(-0.0952777910691, 0.0657605426344, 0.993276242322), (-0.0714644663135, -0.9956927745, 0.0590654625151), (0.992882154429, -0.0653563297625, 0.0995669502217)-115.358282075, -92.3023397585, 208.450747556
21given(0.0760757175843, -0.104271836749, -0.991634947577), (-0.0583934544564, -0.993276035582, 0.0999646018134), (-0.995390722114, 0.0503001113327, -0.0816529799164)-0.136268848283, -99.6097850594, -105.241186737
22given(-0.988752655629, 0.043623209199, -0.143056637757), (0.0641800374465, 0.987727178191, -0.142393624352), (0.13508926227, -0.149973454591, -0.979417609673)-102.689722147, 15.1363448894, 113.293088221

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Components

#1: Protein
Sialic acid-binding periplasmic protein SiaP


Mass: 33991.613 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: siaP, VC_1779 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KR64
#2: Antibody
VHH_VcP#2


Mass: 13483.857 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY
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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Sodium HEPES, pH 7.0, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.81→34.24 Å / Num. obs: 171247 / % possible obs: 99.05 % / Redundancy: 2 % / Biso Wilson estimate: 51.31 Å2 / CC1/2: 0.994 / Net I/σ(I): 0.06463
Reflection shellResolution: 2.81→2.91 Å / Rmerge(I) obs: 0.3428 / Num. unique obs: 17066 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→34.24 Å / SU ML: 0.3882 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 2008 1.17 %
Rwork0.2338 169239 -
obs0.2342 171247 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.14 Å2
Refinement stepCycle: LAST / Resolution: 2.81→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39703 0 276 0 39979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016540765
X-RAY DIFFRACTIONf_angle_d1.812555152
X-RAY DIFFRACTIONf_chiral_restr0.09826072
X-RAY DIFFRACTIONf_plane_restr0.01587163
X-RAY DIFFRACTIONf_dihedral_angle_d8.37465483
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.02598437258
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.03155070503
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.04257163787
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS1.08995471545
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS1.12378297807
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS1.08650339405
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS1.08364326942
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS1.07190018287
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS1.0400291535
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS1.14300029348
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS1.02842173799
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.758854372689
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.882683812262
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.937942739734
ens_2d_5BBX-RAY DIFFRACTIONTorsion NCS0.816043314653
ens_2d_6BBX-RAY DIFFRACTIONTorsion NCS0.911803605484
ens_2d_7BBX-RAY DIFFRACTIONTorsion NCS0.91959035255
ens_2d_8BBX-RAY DIFFRACTIONTorsion NCS0.897217801877
ens_2d_9BBX-RAY DIFFRACTIONTorsion NCS0.870928380677
ens_2d_10BBX-RAY DIFFRACTIONTorsion NCS0.84465043126
ens_2d_11BBX-RAY DIFFRACTIONTorsion NCS0.985436385804
ens_2d_12BBX-RAY DIFFRACTIONTorsion NCS0.855592732721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.35831440.308312072X-RAY DIFFRACTION99.34
2.88-2.950.34521430.297512054X-RAY DIFFRACTION99.42
2.95-3.040.32991400.281112011X-RAY DIFFRACTION99.24
3.04-3.140.34571410.274712094X-RAY DIFFRACTION99.24
3.14-3.250.32731440.276712087X-RAY DIFFRACTION99.36
3.25-3.380.27941410.260812087X-RAY DIFFRACTION98.91
3.38-3.540.24551440.241811803X-RAY DIFFRACTION97.53
3.54-3.720.3151440.234512220X-RAY DIFFRACTION99.89
3.72-3.950.26111440.229412111X-RAY DIFFRACTION99.79
3.96-4.260.2621450.208512150X-RAY DIFFRACTION99.59
4.26-4.690.18871450.189812143X-RAY DIFFRACTION99.39
4.69-5.360.21041430.20312121X-RAY DIFFRACTION99.1
5.36-6.750.27231430.243112015X-RAY DIFFRACTION97.84
6.75-34.240.25751470.209812271X-RAY DIFFRACTION98.85

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