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- PDB-8cp7: Structure of the disulfide-locked substrate binding protein HiSiaP. -

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Basic information

Entry
Database: PDB / ID: 8cp7
TitleStructure of the disulfide-locked substrate binding protein HiSiaP.
ComponentsSialic acid-binding periplasmic protein SiaP
KeywordsSUGAR BINDING PROTEIN / Substrate binding protein / TRAP / sialic acid
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, Y. / Peter, M.F. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA 6805/5-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP.
Authors: Peter, M.F. / Ruland, J.A. / Kim, Y. / Hendricks, P. / Schneberger, N. / Siebrasse, J.P. / Thomas, G.H. / Kubitscheck, U. / Hagelueken, G.
History
DepositionMar 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1354
Polymers34,6951
Non-polymers4403
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-33 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.083, 89.451, 90.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-402-

ZN

21A-505-

HOH

31A-549-

HOH

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Components

#1: Protein Sialic acid-binding periplasmic protein SiaP / Extracytoplasmic solute receptor protein SiaP / N-acetylneuraminic-binding protein / Neu5Ac-binding protein


Mass: 34695.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: siaP, HI_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: P44542
#2: 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.: 1 / 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc chloride, 0.1 M Sodium acetate, pH 5.0, 20% w/v PEG 6000

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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: 0.826554 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826554 Å / Relative weight: 1
ReflectionResolution: 1.9→42.04 Å / Num. obs: 26990 / % possible obs: 99.02 % / Redundancy: 2 % / Biso Wilson estimate: 33.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0289 / Net I/σ(I): 14.84
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 2437 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
PHENIXdev_4788phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.04 Å / SU ML: 0.2686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1471 5.45 %
Rwork0.2101 25519 -
obs0.2127 26990 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 23 134 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032553
X-RAY DIFFRACTIONf_angle_d1.03343457
X-RAY DIFFRACTIONf_chiral_restr0.0592382
X-RAY DIFFRACTIONf_plane_restr0.0084450
X-RAY DIFFRACTIONf_dihedral_angle_d19.2088970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.35941420.34412295X-RAY DIFFRACTION99.43
1.96-2.030.35031210.30592290X-RAY DIFFRACTION99.34
2.03-2.110.34251300.26742329X-RAY DIFFRACTION99.68
2.11-2.210.32331440.24772282X-RAY DIFFRACTION99.75
2.21-2.330.35111290.24172327X-RAY DIFFRACTION99.88
2.33-2.470.30331180.23612334X-RAY DIFFRACTION99.43
2.47-2.660.26371340.22862124X-RAY DIFFRACTION92.01
2.66-2.930.25151340.2112354X-RAY DIFFRACTION99.92
2.93-3.350.25711280.20522351X-RAY DIFFRACTION100
3.35-4.220.24921330.1872386X-RAY DIFFRACTION100
4.22-42.040.21041580.18192447X-RAY DIFFRACTION99.69

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