[English] 日本語
Yorodumi
- PDB-4mnp: Structure of the Sialic Acid Binding Protein from Fusobacterium N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mnp
TitleStructure of the Sialic Acid Binding Protein from Fusobacterium Nucleatum subsp. nucleatum ATCC 25586
ComponentsN-acetylneuraminate-binding protein
KeywordsSUGAR BINDING PROTEIN / Sialic Acid binding protein / 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 / N-acetylneuraminate-binding protein
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsThanuja, G. / Ramaswamy, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site.
Authors: Gangi Setty, T. / Cho, C. / Govindappa, S. / Apicella, M.A. / Ramaswamy, S.
#1: Journal: 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
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
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 1.3Sep 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylneuraminate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6822
Polymers35,3731
Non-polymers3091
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.841, 58.729, 111.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein N-acetylneuraminate-binding protein


Mass: 35372.641 Da / Num. of mol.: 1 / Fragment: UNP residues 24-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN1472, SiaP / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RDN9
#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 / N-Acetylneuraminic 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 / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 277 K / pH: 8.5
Details: Drops were setup with equal volume of protein and 0.2M MgCl2, 0.1M TRIS 8.5, 35% PEG 4000 (crystallization buffer) and suspended over 100ul of crystallization buffer., VAPOR DIFFUSION, ...Details: Drops were setup with equal volume of protein and 0.2M MgCl2, 0.1M TRIS 8.5, 35% PEG 4000 (crystallization buffer) and suspended over 100ul of crystallization buffer., VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.056→41.84 Å / Num. obs: 17627 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
AMoREphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B50

3b50


Resolution: 2.5→40.47 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.19 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 491 4.91 %
Rwork0.213 --
obs0.215 17627 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 21 141 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022476
X-RAY DIFFRACTIONf_angle_d0.5373328
X-RAY DIFFRACTIONf_dihedral_angle_d13.65934
X-RAY DIFFRACTIONf_chiral_restr0.021368
X-RAY DIFFRACTIONf_plane_restr0.002424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65670.29641520.26312876X-RAY DIFFRACTION99
2.6567-2.86170.32551380.26152825X-RAY DIFFRACTION98
2.8617-3.14960.3581520.24762870X-RAY DIFFRACTION98
3.1496-3.60510.27451530.20542900X-RAY DIFFRACTION99
3.6051-4.54110.20491440.18132873X-RAY DIFFRACTION99
4.5411-40.47120.2021500.19442873X-RAY DIFFRACTION99

+
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