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- PDB-2v4c: Structure of sialic acid binding protein (SiaP) in the presence of KDN -

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Basic information

Entry
Database: PDB / ID: 2v4c
TitleStructure of sialic acid binding protein (SiaP) in the presence of KDN
ComponentsSIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORT / TRANSPORT PROTEIN ESR / TRAP
Function / homology
Function and homology information


: / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
deamino-beta-neuraminic acid / Sialic acid-binding periplasmic protein SiaP
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFischer, M. / Hubbard, R.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Water networks can determine the affinity of ligand binding to proteins.
Authors: Darby, J.F. / Hopkins, A.P. / Shimizu, S. / Roberts, S.M. / Brannigan, J.A. / Turkenburg, J.P. / Thomas, G.H. / Hubbard, R.E. / Fischer, M.
History
DepositionSep 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_database_status
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.src_method / _pdbx_database_status.status_code_sf
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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: SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8862
Polymers34,6181
Non-polymers2681
Water6,233346
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.399, 74.502, 86.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP / SIALIC ACID BINDING PROTEIN / N-ACETYLNEURAMINIC -BINDING PROTEIN / NEU5AC-BINDING PROTEIN / ...SIALIC ACID BINDING PROTEIN / N-ACETYLNEURAMINIC -BINDING PROTEIN / NEU5AC-BINDING PROTEIN / EXTRACYTOPLASMIC SOLUTE RECEPTOR PROTEIN SIAP


Mass: 34618.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS PAH16 / References: UniProt: P44542
#2: Sugar ChemComp-KDN / deamino-beta-neuraminic acid / beta-deaminoneuraminic acid / 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid / sialic acid


Type: D-saccharide, beta linking / Mass: 268.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H16O9
IdentifierTypeProgram
DKdnpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
2-keto-3-deoxy-b-D-nonulopyranosic acidCOMMON NAMEGMML 1.0
b-D-KdnpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdnSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7
Details: 36 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL, 10 MM KDN, PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0 28.5% PEG 6K); TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9755
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 34122 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.43 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B50

3b50


Resolution: 1.7→41.56 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.03 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19397 1711 5 %RANDOM
Rwork0.14309 ---
obs0.1457 32329 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 18 346 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222574
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9763500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4275332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14225.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99815463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.095155
X-RAY DIFFRACTIONr_chiral_restr0.1150.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211948
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3591.51578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15322547
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2683996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1534.5941
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 101
Rwork0.208 2125

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