[English] 日本語
Yorodumi
- PDB-4zxk: Carbohydrate binding domain from Streptococcus pneumoniae NanA si... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zxk
TitleCarbohydrate binding domain from Streptococcus pneumoniae NanA sialidase
ComponentsSialidase A
KeywordsSUGAR BINDING PROTEIN / carbohydrate-binding module / sialic acid binding
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process / extracellular region
Similarity search - Function
Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Sialidase superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsYang, L. / Connaris, H. / Potter, J.A. / Taylor, G.L.
CitationJournal: To Be Published
Title: Carbohydrate binding domain from Streptococcus pneumoniae NanA sialidase
Authors: Yang, L. / Connaris, H. / Potter, J.A. / Taylor, G.L.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sialidase A
B: Sialidase A


Theoretical massNumber of molelcules
Total (without water)42,1332
Polymers42,1332
Non-polymers00
Water5,729318
1
A: Sialidase A


Theoretical massNumber of molelcules
Total (without water)21,0671
Polymers21,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sialidase A


Theoretical massNumber of molelcules
Total (without water)21,0671
Polymers21,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.234, 66.984, 66.792
Angle α, β, γ (deg.)90.000, 92.430, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Sialidase A / Neuraminidase A


Mass: 21066.666 Da / Num. of mol.: 2 / Fragment: UNP residues 121-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: nanA / Production host: Escherichia coli (E. coli) / References: UniProt: P62575, exo-alpha-sialidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: DL-malic acid, MES, tris base, PEG 1500 valine / PH range: 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: May 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 29236 / % possible obs: 96.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.031 / Χ2: 2.91 / Net I/av σ(I): 43.895 / Net I/σ(I): 49.1 / Num. measured all: 72568
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.84-1.8720.06911233.3173.9
1.87-1.912.30.06313943.27194
1.91-1.942.40.0614883.36598.9
1.94-1.982.40.05314893.25398.5
1.98-2.032.50.04914893.29198.5
2.03-2.072.50.0514633.44798.4
2.07-2.122.50.04914443.40398.4
2.12-2.182.40.04715063.24998.1
2.18-2.252.50.04314803.04999
2.25-2.322.50.04315003.05499.1
2.32-2.42.50.03914932.82498.9
2.4-2.52.50.03914612.88498.5
2.5-2.612.50.03714952.74798.4
2.61-2.752.50.03514672.72898.5
2.75-2.922.60.03214932.598.4
2.92-3.152.60.0314872.58198.4
3.15-3.462.60.02614922.2898.3
3.46-3.962.60.02415022.15298
3.96-4.992.60.02414822.21897.1
4.99-502.60.02314883.13795.1

-
Processing

Software
NameVersionClassification
SCALEPACKHKL2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SLI

2sli


Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2272 / WRfactor Rwork: 0.1792 / FOM work R set: 0.8625 / SU B: 4.985 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1481 / SU Rfree: 0.1366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1481 5.1 %RANDOM
Rwork0.1624 ---
obs0.1647 27743 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.19 Å2 / Biso mean: 17.495 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.53 Å2
2---0.19 Å20 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 0 318 3280
Biso mean---25.52 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023086
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9544185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26824.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80615551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7241522
X-RAY DIFFRACTIONr_chiral_restr0.1640.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212360
LS refinement shellResolution: 1.839→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 96 -
Rwork0.197 1673 -
all-1769 -
obs--80.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3958-0.380.44471.44830.18211.59070.0319-0.04130.04310.01790.007-0.07590.02790.0599-0.03890.0244-0.01250.00320.0392-0.00780.00637.98312.41130.048
21.0942-0.20030.31291.34850.09131.26930.0122-0.0282-0.01010.00380.0154-0.11190.03840.07-0.02750.0231-0.0057-0.00070.0298-0.00590.011-10.16713.148-3.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A118 - 305
2X-RAY DIFFRACTION2B118 - 305

+
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