[English] 日本語
Yorodumi
- PDB-4v1r: Structure of a selenomethionine derivative of the GH76 alpha- man... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v1r
TitleStructure of a selenomethionine derivative of the GH76 alpha- mannanase BT2949 Bacteroides thetaiotaomicron
ComponentsALPHA-1,6-MANNANASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / BACTEROIDES / POLYSACCHARIDE UTILISATION / ENZYME-CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / Alpha-1,6-mannanase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsThompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the Gh76 Alpha-Mannanase Homolog, Bt2949, from the Gut Symbiont Bacteroides Thetaiotaomicron
Authors: Thompson, A.J. / Cuskin, F. / Spears, R.J. / Dabin, J. / Turkenburg, J.P. / Gilbert, H.J. / Davies, G.J.
History
DepositionOct 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-1,6-MANNANASE
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1147
Polymers91,5392
Non-polymers5745
Water18,3211017
1
A: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1945
Polymers45,7701
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,6-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9202
Polymers45,7701
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.695, 120.743, 126.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-2166-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00015, 0.00036), (0.000146, -0.9999, -0.01185), (0.000362, -0.01185, 0.9999)
Vector: 122.5, 1.557, -8.216)

-
Components

#1: Protein ALPHA-1,6-MANNANASE


Mass: 45769.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q8A3K5, mannan endo-1,6-alpha-mannosidase
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.29 % / Description: NONE
Crystal growpH: 7.2 / Details: 1.5 M AMMONIUM TARTRATE PH 7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97926
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→48.5 Å / Num. obs: 115956 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 7.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDE PIPELINEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→126.16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.701 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.16814 5813 5 %RANDOM
Rwork0.14768 ---
obs0.14872 110076 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.303 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--1.96 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→126.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5801 0 38 1017 6856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026158
X-RAY DIFFRACTIONr_bond_other_d0.0030.025524
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.948409
X-RAY DIFFRACTIONr_angle_other_deg0.942312729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35324.702302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0811520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027138
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021530
X-RAY DIFFRACTIONr_nbd_refined0.2660.22472
X-RAY DIFFRACTIONr_nbd_other0.1680.25460
X-RAY DIFFRACTIONr_nbtor_refined0.1910.23121
X-RAY DIFFRACTIONr_nbtor_other0.0820.22647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.283
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1110.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.9422943
X-RAY DIFFRACTIONr_mcbond_other1.311.942942
X-RAY DIFFRACTIONr_mcangle_it1.9322.93690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1892.1773215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.433.1734693
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 445 -
Rwork0.207 8009 -
obs--99.94 %

+
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