[English] 日本語
Yorodumi
- PDB-3b50: Structure of H. influenzae sialic acid binding protein bound to N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b50
TitleStructure of H. influenzae sialic acid binding protein bound to Neu5Ac.
ComponentsSialic acid-binding periplasmic protein siaP
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / TRAP / Sugar transport / Transport
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsRamaswamy, S. / Coussens, N.P. / Apicella, M.A. / Johnston, J.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019
Authors: Johnston, J.W. / Coussens, N.P. / Allen, S. / Houtman, J.C. / Turner, K.H. / Zaleski, A. / Ramaswamy, S. / Gibson, B.W. / Apicella, M.A.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,8992
Polymers34,5901
Non-polymers3091
Water8,557475
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.527, 74.598, 86.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 34590.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: NTHi 2019 / Gene: siaP / 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: 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


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 37 mg/mL SiaP in 20 mM HEPES, 10 mM NaCl, 10 mM Neu5Ac, pH 8.0 and reservoir solution (100 mM MES, 30% w/v PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 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: 1.4→36.37 Å / Num. obs: 61154 / % possible obs: 99.6 % / Redundancy: 7.03 % / Rmerge(I) obs: 0.079 / Χ2: 0.99 / Net I/σ(I): 10.1 / Scaling rejects: 3250
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.4-1.455.340.4942.53168558791.3996.8
1.45-1.517.050.4283.14267860001.3299.7
1.51-1.587.170.3463.94383560581.299.8
1.58-1.667.20.2834.74389260561.1599.9
1.66-1.767.230.2275.64446661041.08100
1.76-1.97.270.1896.74467861060.99100
1.9-2.097.310.13594490161130.86100
2.09-2.397.30.08113.84528461530.74100
2.39-3.027.290.06915.84569162120.7100
3.02-36.377.070.03231.84605464730.6599.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→36.37 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3094 5.1 %RANDOM
Rwork0.161 ---
obs0.163 61075 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 21 475 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222551
X-RAY DIFFRACTIONr_bond_other_d0.0050.021729
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9793455
X-RAY DIFFRACTIONr_angle_other_deg0.9234267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02326120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.879156
X-RAY DIFFRACTIONr_chiral_restr0.2380.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
X-RAY DIFFRACTIONr_nbd_refined0.2360.2558
X-RAY DIFFRACTIONr_nbd_other0.1770.21883
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21283
X-RAY DIFFRACTIONr_nbtor_other0.0890.21255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2352
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.261
X-RAY DIFFRACTIONr_mcbond_it1.4141.52039
X-RAY DIFFRACTIONr_mcbond_other0.6421.5630
X-RAY DIFFRACTIONr_mcangle_it1.68322517
X-RAY DIFFRACTIONr_scbond_it2.9131159
X-RAY DIFFRACTIONr_scangle_it3.8024.5931
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 221 -
Rwork0.271 4065 -
all-4286 -
obs--95.63 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more