[English] 日本語
Yorodumi
- PDB-4xso: Crystal structure of apo-form Alr3699/HepE from Anabaena sp. stra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xso
TitleCrystal structure of apo-form Alr3699/HepE from Anabaena sp. strain PCC 7120
ComponentsAlr3699 protein
KeywordsTRANSFERASE / GT-B fold / glycosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsWang, X.P. / Dai, Y.N. / Jiang, Y.L. / Cheng, W. / Chen, Y.X. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
CitationJournal: Glycobiology / Year: 2016
Title: Structural and enzymatic analyses of a glucosyltransferase Alr3699/HepE involved in Anabaena heterocyst envelop polysaccharide biosynthesis
Authors: Wang, X.P. / Jiang, Y.L. / Dai, Y.N. / Cheng, W. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Alr3699 protein
A: Alr3699 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1156
Polymers84,7472
Non-polymers3684
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-17 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.289, 133.469, 142.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Alr3699 protein


Mass: 42373.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: glycerol
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / UTEX 2576 / Gene: alr3699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YQW3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M ammonium citrate tribasic pH 7.0, 0.1 M Bis-Tris propane pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 48403 / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.56
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.96 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→38.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.444 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24567 2467 5.1 %RANDOM
Rwork0.19446 ---
obs0.19711 45852 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.148 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2---1.1 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2.01→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 24 149 5733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195682
X-RAY DIFFRACTIONr_bond_other_d0.0010.025588
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9597714
X-RAY DIFFRACTIONr_angle_other_deg0.874312800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71224.797246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00515940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3081528
X-RAY DIFFRACTIONr_chiral_restr0.1080.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021294
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_it3.4643.7732908
X-RAY DIFFRACTIONr_mcbond_other3.4613.7722907
X-RAY DIFFRACTIONr_mcangle_it4.3355.6353628
X-RAY DIFFRACTIONr_mcangle_other4.3345.6373629
X-RAY DIFFRACTIONr_scbond_it4.9434.3672774
X-RAY DIFFRACTIONr_scbond_other4.9374.3672774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.076.3414087
X-RAY DIFFRACTIONr_long_range_B_refined8.62331.1756345
X-RAY DIFFRACTIONr_long_range_B_other8.63731.0416320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 181 -
Rwork0.243 3363 -
obs--96.41 %

+
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