[English] 日本語
Yorodumi
- PDB-7l74: Crystal structure of Beta-hexosyl transferase from Hamamotoa (Spo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l74
TitleCrystal structure of Beta-hexosyl transferase from Hamamotoa (Sporobolomyces) singularis bound to TRIS
ComponentsBeta-hexosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


beta-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-galactosidase-like enzyme
Similarity search - Component
Biological speciesHamamotoa singularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDagher, S.F. / Edwards, B.F.P. / Meilleur, F. / Bruno-Barcena, J.M.
Citation
Journal: To Be Published
Title: Structure and mutagenic analysis of the Beta-hexosyltransferase from Hamamotoa (Sporobolomyces) singularis
Authors: Dagher, S.F. / Edwards, B.F.P. / Meilleur, F. / Bruno-Barcena, J.M.
#1: Journal: Microbiology (Reading) / Year: 2016
Title: A novel N-terminal region of the membrane Beta-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris.
Authors: Dagher, S.F. / Bruno-Barcena, J.M.
#2: Journal: Appl Environ Microbiol / Year: 2013
Title: Heterologous expression of a bioactive Beta-hexosyltransferase, an enzyme producer of prebiotics, from Sporobolomyces singularis.
Authors: Dagher, S.F. / Azcarate-Peril, M.A. / Bruno-Barcena, J.M.
History
DepositionDec 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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: Beta-hexosyltransferase
B: Beta-hexosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,85213
Polymers129,1722
Non-polymers3,68011
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint21 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.319, 63.209, 105.006
Angle α, β, γ (deg.)90.000, 100.420, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 54 - 593 / Label seq-ID: 32 - 571

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Beta-hexosyltransferase


Mass: 64586.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hamamotoa singularis (fungus) / Gene: bglA / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q564N5
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Well: 30% PEG 4000, 0.1 M HEPES 7.5, 0.2 M CaCl2 Hanging Drop: 1:1 Protein:Well

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→29.97 Å / Num. obs: 59376 / % possible obs: 98.4 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.076 / Rrim(I) all: 0.159 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.374.10.6863414782930.7080.3770.7842.594.8
7.12-29.953.70.044734819650.9950.0260.05124.197.5

-
Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: raptorX structure prediction

Resolution: 2.25→29.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.923 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2934 4.9 %RANDOM
Rwork0.1892 ---
obs0.1914 56424 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.05 Å2 / Biso mean: 28.069 Å2 / Biso min: 10.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0.03 Å2
2--0.31 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2.25→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8583 0 241 523 9347
Biso mean--56.58 31.13 -
Num. residues----1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139108
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177843
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.6812466
X-RAY DIFFRACTIONr_angle_other_deg1.3611.60718228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.71651081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44823.044473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.063151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.291536
X-RAY DIFFRACTIONr_chiral_restr0.090.21183
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022026
Refine LS restraints NCS

Ens-ID: 1 / Number: 18231 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 214 -
Rwork0.27 3834 -
all-4048 -
obs--90.38 %
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)
11.05120.33990.10931.19210.05390.6829-0.04370.13940.1277-0.18170.04010.06040.0048-0.06540.00360.0329-0.0268-0.00970.11260.02350.016334.1511.30430.729
20.96410.244-0.25351.3747-0.09720.5914-0.0360.0924-0.0645-0.16490.0456-0.11180.04230.0083-0.00950.0241-0.01840.01450.0864-0.0220.014982.0259.80628.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 594
2X-RAY DIFFRACTION2B54 - 595

+
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