[English] 日本語
Yorodumi
- PDB-8cp7: Structure of the disulfide-locked substrate binding protein HiSiaP. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cp7
TitleStructure of the disulfide-locked substrate binding protein HiSiaP.
ComponentsSialic acid-binding periplasmic protein SiaP
KeywordsSUGAR BINDING PROTEIN / Substrate binding protein / TRAP / sialic acid
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / N-acetyl-beta-neuraminic acid / Sialic acid-binding periplasmic protein SiaP
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, Y. / Peter, M.F. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA 6805/5-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Conformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP.
Authors: Peter, M.F. / Ruland, J.A. / Kim, Y. / Hendricks, P. / Schneberger, N. / Siebrasse, J.P. / Thomas, G.H. / Kubitscheck, U. / Hagelueken, G.
History
DepositionMar 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)35,1354
Polymers34,6951
Non-polymers4403
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-33 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.083, 89.451, 90.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-402-

ZN

21A-505-

HOH

31A-549-

HOH

-
Components

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


Mass: 34695.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: siaP, HI_0146 / 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: obtained synthetically / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc chloride, 0.1 M Sodium acetate, pH 5.0, 20% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826554 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826554 Å / Relative weight: 1
ReflectionResolution: 1.9→42.04 Å / Num. obs: 26990 / % possible obs: 99.02 % / Redundancy: 2 % / Biso Wilson estimate: 33.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0289 / Net I/σ(I): 14.84
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 2437 / CC1/2: 0.721

-
Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
PHENIXdev_4788phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.04 Å / SU ML: 0.2686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1471 5.45 %
Rwork0.2101 25519 -
obs0.2127 26990 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 23 134 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032553
X-RAY DIFFRACTIONf_angle_d1.03343457
X-RAY DIFFRACTIONf_chiral_restr0.0592382
X-RAY DIFFRACTIONf_plane_restr0.0084450
X-RAY DIFFRACTIONf_dihedral_angle_d19.2088970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.35941420.34412295X-RAY DIFFRACTION99.43
1.96-2.030.35031210.30592290X-RAY DIFFRACTION99.34
2.03-2.110.34251300.26742329X-RAY DIFFRACTION99.68
2.11-2.210.32331440.24772282X-RAY DIFFRACTION99.75
2.21-2.330.35111290.24172327X-RAY DIFFRACTION99.88
2.33-2.470.30331180.23612334X-RAY DIFFRACTION99.43
2.47-2.660.26371340.22862124X-RAY DIFFRACTION92.01
2.66-2.930.25151340.2112354X-RAY DIFFRACTION99.92
2.93-3.350.25711280.20522351X-RAY DIFFRACTION100
3.35-4.220.24921330.1872386X-RAY DIFFRACTION100
4.22-42.040.21041580.18192447X-RAY DIFFRACTION99.69

+
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