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- PDB-5z99: Crystal structure of Sialic acid Binding protein from Haemophilus... -

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Basic information

Entry
Database: PDB / ID: 5z99
TitleCrystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac
ComponentsPutative ABC transporter periplasmic binding protein
KeywordsSUGAR BINDING PROTEIN / three domain proteins / sialic acid Neu5Gc / bacteria / molecular mimicry / adhesion / cell signaling / nutrition
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
N-acetyl-beta-neuraminic acid / ABC transporter periplasmic binding protein
Similarity search - Component
Biological speciesHaemophilus ducreyi 35000HP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsSubramanian, R. / Setty, T.G.
Funding support India, 2items
OrganizationGrant numberCountry
SR/SO/BB-19/2010 India
BT/IN/Sweden/41/SR/2013 India
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Molecular characterization of the interaction of sialic acid with the periplasmic binding protein fromHaemophilus ducreyi.
Authors: Gangi Setty, T. / Mowers, J.C. / Hobbs, A.G. / Maiya, S.P. / Syed, S. / Munson Jr., R.S. / Apicella, M.A. / Subramanian, R.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ABC transporter periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3792
Polymers54,0691
Non-polymers3091
Water10,124562
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-1 kcal/mol
Surface area18310 Å2
Unit cell
Length a, b, c (Å)73.368, 89.630, 90.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative ABC transporter periplasmic binding protein


Mass: 54069.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi 35000HP (bacteria) / Strain: 35000HP / ATCC 700724 / Gene: HD_1669 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7VL18
#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 / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 20mM MES, 60mM NaCl, 30% PEG 1500, pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.49→19.52 Å / Num. obs: 93977 / % possible obs: 96.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Net I/σ(I): 19 / Num. measured all: 604746 / Scaling rejects: 554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.49-1.525.50.5382320742370.8070.2370.5914.988.6
8.18-19.526.30.0238876170.9990.0080.02193.492

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YYB

5yyb


Resolution: 1.494→19.518 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 4864 5.18 %
Rwork0.1688 89067 -
obs0.1701 93931 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.3 Å2 / Biso mean: 18.1749 Å2 / Biso min: 6.97 Å2
Refinement stepCycle: final / Resolution: 1.494→19.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 39 562 4425
Biso mean--10.94 29.01 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054116
X-RAY DIFFRACTIONf_angle_d0.7965639
X-RAY DIFFRACTIONf_chiral_restr0.08631
X-RAY DIFFRACTIONf_plane_restr0.005730
X-RAY DIFFRACTIONf_dihedral_angle_d17.9281504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4936-1.51050.29241210.30272571269284
1.5105-1.52830.29331660.24932951311797
1.5283-1.54690.24891710.23512979315098
1.5469-1.56650.25741710.22752968313997
1.5665-1.58710.26671510.2092947309898
1.5871-1.60880.23051710.20072979315098
1.6088-1.63180.22791730.19962984315797
1.6318-1.65620.22811870.19092952313998
1.6562-1.6820.20721450.18582969311497
1.682-1.70960.2421760.19262979315597
1.7096-1.7390.2131810.17632950313198
1.739-1.77060.19731440.16812977312197
1.7706-1.80470.1911810.16372951313297
1.8047-1.84150.20131590.16452956311596
1.8415-1.88150.22491520.16822975312797
1.8815-1.92520.21881310.16582982311397
1.9252-1.97330.19181940.16462910310496
1.9733-2.02660.18591610.17692935309696
2.0266-2.08620.19411310.16362934306595
2.0862-2.15350.18891520.16152925307795
2.1535-2.23030.19351520.16032879303193
2.2303-2.31950.18591520.16272918307095
2.3195-2.42490.17671670.16212938310595
2.4249-2.55240.19891730.17452919309295
2.5524-2.7120.20841480.17263021316996
2.712-2.92070.19291750.17652983315897
2.9207-3.21350.18731840.17053027321197
3.2135-3.67580.18461350.16423151328699
3.6758-4.6210.15921760.135131703346100
4.621-19.52010.16551840.146732873471100

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