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- PDB-2wx9: Crystal structure of the sialic acid binding periplasmic protein SiaP -

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Basic information

Entry
Database: PDB / ID: 2wx9
TitleCrystal structure of the sialic acid binding periplasmic protein SiaP
ComponentsSIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP
KeywordsTRANSPORT PROTEIN / SUGAR TRANSPORT / TRAP TRANSPORTER
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
N-glycolyl-beta-neuraminic acid / Sialic acid-binding periplasmic protein SiaP
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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
DepositionNov 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 18, 2017Group: Atomic model / Structure summary / Category: atom_site / atom_site_anisotrop / entity
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 2.1Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Sep 25, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._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 / _pdbx_database_status.status_code_sf
Revision 3.0Jul 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 3.1Dec 20, 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)35,4012
Polymers35,0761
Non-polymers3251
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 74.490, 87.480
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 / N-ACETYLNEURAMINIC-BINDING PROTEIN / NEU5AC-BINDING PROTEIN / EXTRACYTOPLASMIC SOLUTE RECEPTOR PROTEIN SIAP


Mass: 35075.641 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Plasmid: PAH16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P44542
#2: Sugar ChemComp-NGE / N-glycolyl-beta-neuraminic acid / N-glycolylneuraminic acid / sialic acid


Type: D-saccharide, beta linking / Mass: 325.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO10
IdentifierTypeProgram
DNeup5GcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-glycolyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5GcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5GcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 34 TO ASN

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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: 45 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7
Details: 36 MG/ML SIAP (IN 20 MM HEPES, 10 MM NACL,AND NEU5GC PH 8.0) AND EQUAL VOLUME OF RESERVOIR SOLUTION (100MM MES PH 6.0, 28.5% PEG 6K, 3% W/V 1,5-DIAMINOPENTANE DIHYDROCHLORIDE) TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.37→32.25 Å / Num. obs: 62379 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V4C

2v4c


Resolution: 1.37→32.25 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.607 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.158 3336 5.1 %2V4C
Rwork0.116 ---
obs0.118 62379 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.37→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 22 548 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222636
X-RAY DIFFRACTIONr_bond_other_d0.0020.021781
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9763582
X-RAY DIFFRACTIONr_angle_other_deg2.2933.0014383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93925.968124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1815477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.021156
X-RAY DIFFRACTIONr_chiral_restr0.1180.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212986
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02506
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_it1.6681.51618
X-RAY DIFFRACTIONr_mcbond_other1.2881.5645
X-RAY DIFFRACTIONr_mcangle_it2.41922614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.66331018
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1084.5962
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.6634417
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 258 -
Rwork0.193 4579 -
obs--99.98 %

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