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- PDB-6h76: SiaP in complex with Neu5Ac (RT) -

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Basic information

Entry
Database: PDB / ID: 6h76
TitleSiaP in complex with Neu5Ac (RT)
ComponentsSialic acid-binding periplasmic protein SiaP
KeywordsTRANSPORT PROTEIN / TRAP transporter / Sialic acid
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-acetyl-beta-neuraminic acid / Sialic acid-binding periplasmic protein SiaP
Similarity search - Component
Biological speciesHaemophilus influenzae Rd KW20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsFischer, M. / Darby, J.F. / Brannigan, J.A. / Turkenburg, J. / Hubbard, R.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBBC509807 United Kingdom
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
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
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
Revision 1.2Oct 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.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialic acid-binding periplasmic protein SiaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6796
Polymers35,0331
Non-polymers6465
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-80 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.788, 75.310, 87.774
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 / Extracytoplasmic solute receptor protein SiaP / N-acetylneuraminic-binding protein / Neu5Ac-binding protein


Mass: 35032.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria)
Gene: siaP, HI_0146 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: isolated from a genetically manipulated source
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 28.5% PEG 6000, 100 mM MES pH 6.0, 0.1 M CsCl, 5% Jeffamine

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature data collection
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→57.16 Å / Num. obs: 51316 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2510 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→57.16 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.854 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15454 2589 5.1 %RANDOM
Rwork0.11157 ---
obs0.11379 48667 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0 Å2
2---1.06 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.5→57.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 25 172 2625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192696
X-RAY DIFFRACTIONr_bond_other_d0.0010.022454
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9753675
X-RAY DIFFRACTIONr_angle_other_deg0.9735761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09126.094128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.076155
X-RAY DIFFRACTIONr_chiral_restr0.110.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213090
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
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_it2.3862.0881330
X-RAY DIFFRACTIONr_mcbond_other2.3782.0871329
X-RAY DIFFRACTIONr_mcangle_it2.8583.1521689
X-RAY DIFFRACTIONr_mcangle_other2.863.1541690
X-RAY DIFFRACTIONr_scbond_it3.9112.6771366
X-RAY DIFFRACTIONr_scbond_other3.912.6771366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5483.7661983
X-RAY DIFFRACTIONr_long_range_B_refined4.225.9543007
X-RAY DIFFRACTIONr_long_range_B_other4.19925.9533008
X-RAY DIFFRACTIONr_rigid_bond_restr3.34735150
X-RAY DIFFRACTIONr_sphericity_free23.4215134
X-RAY DIFFRACTIONr_sphericity_bonded11.93455123
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 185 -
Rwork0.215 3575 -
obs--99.21 %

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