[English] 日本語
Yorodumi
- PDB-3vmp: Crystal structure of dextranase from Streptococcus mutans in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vmp
TitleCrystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside
ComponentsDextranase
KeywordsHYDROLASE / TIM Barrel / immunoglobrin fold / Greek-key motif / Glycoside hydrolase family 66
Function / homology
Function and homology information


dextranase / dextranase activity / extracellular region / membrane
Similarity search - Function
Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-hydroxypentyl alpha-D-glucopyranoside / PHOSPHATE ION / Dextranase / Dextranase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSuzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Okuyama, M. / Mori, H. / Funane, K. / Kimura, A.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66
Authors: Suzuki, N. / Kim, Y.M. / Fujimoto, Z. / Momma, M. / Okuyama, M. / Mori, H. / Funane, K. / Kimura, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans.
Authors: Suzuki, N. / Kim, Y.M. / Fujimoto, Z. / Momma, M. / Kang, H.K. / Funane, K. / Okuyama, M. / Mori, H. / Kimura, A.
History
DepositionDec 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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: Dextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9583
Polymers72,5961
Non-polymers3612
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.428, 89.966, 62.842
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dextranase


Mass: 72596.383 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 100-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 25175 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F5BA50, UniProt: Q54443*PLUS, dextranase
#2: Sugar ChemComp-E5G / 5-hydroxypentyl alpha-D-glucopyranoside / 5-hydroxypentyl alpha-D-glucoside / 5-hydroxypentyl D-glucoside / 5-hydroxypentyl glucoside


Type: D-saccharide / Mass: 266.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H22O7
IdentifierTypeProgram
5-hydroxypentyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 30% PEGMME 2000, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→61.41 Å / Num. obs: 45454 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.4 / Num. unique all: 4112 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMN

3vmn


Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.851 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23771 2306 5.1 %RANDOM
Rwork0.19548 ---
obs0.19762 43068 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.537 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å20.42 Å2
2---0.93 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 23 373 5408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9476994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23225.763262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29815847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213969
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9071.53144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59125063
X-RAY DIFFRACTIONr_scbond_it2.51931996
X-RAY DIFFRACTIONr_scangle_it4.0294.51931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.884→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 120 -
Rwork0.246 2247 -
obs--67.69 %

+
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