[English] 日本語
Yorodumi
- PDB-5z74: Crystal structure of alkaline/neutral invertase InvB from Anabaen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z74
TitleCrystal structure of alkaline/neutral invertase InvB from Anabaena sp. PCC 7120 complexed with sucrose
ComponentsAlr0819 protein
KeywordsHYDROLASE / alkaline/neutral invertases / cyanobacteria / glycoside hydrolase family 100 / sucrose hydrolysis
Function / homology
Function and homology information


endo-alpha-N-acetylgalactosaminidase activity / beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 100 / Alkaline and neutral invertase / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
sucrose / beta-fructofuranosidase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsXie, J. / Hu, H.X. / Cai, K. / Yang, F. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural and enzymatic analyses of Anabaena heterocyst-specific alkaline invertase InvB.
Authors: Xie, J. / Hu, H.X. / Cai, K. / Xia, L.Y. / Yang, F. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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
B: Alr0819 protein
A: Alr0819 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9044
Polymers105,2192
Non-polymers6852
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-25 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.946, 82.171, 97.446
Angle α, β, γ (deg.)90.00, 119.13, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Alr0819 protein / Neutral invertase


Mass: 52609.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: invB, alr0819 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YYM9, beta-fructofuranosidase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.7M lithium chloride, 6% polyethylene glycol 6000, 0.1M MES, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2016
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 80206 / % possible obs: 95.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8173 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z73

5z73


Resolution: 1.95→31.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.686 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23854 4009 5 %RANDOM
Rwork0.20828 ---
obs0.20978 76001 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20.19 Å2
2---0.39 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.95→31.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 0 46 184 7238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197240
X-RAY DIFFRACTIONr_bond_other_d0.0050.026920
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9839834
X-RAY DIFFRACTIONr_angle_other_deg0.735315913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40123.855332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.433151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1481546
X-RAY DIFFRACTIONr_chiral_restr0.0620.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021661
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_it1.363.563489
X-RAY DIFFRACTIONr_mcbond_other1.363.5593488
X-RAY DIFFRACTIONr_mcangle_it2.335.3294353
X-RAY DIFFRACTIONr_mcangle_other2.3295.334354
X-RAY DIFFRACTIONr_scbond_it1.5113.843751
X-RAY DIFFRACTIONr_scbond_other1.5113.843751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6385.6495481
X-RAY DIFFRACTIONr_long_range_B_refined4.07629.0938568
X-RAY DIFFRACTIONr_long_range_B_other4.07329.0688519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 270 -
Rwork0.273 5675 -
obs--97.06 %

+
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://pdbjlvh1.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