[English] 日本語
Yorodumi
- PDB-5zla: Crystal structure of mutant C387A of DFA-IIIase from Arthrobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zla
TitleCrystal structure of mutant C387A of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with DFA-III
ComponentsDFA-IIIase C387A mutant
KeywordsHYDROLASE / hydrolyze difructose anhydride / parallel beta helix / endoenzyme
Function / homology
Function and homology information


inulin fructotransferase (DFA-I-forming) / inulin fructotransferase (DFA-I-forming) activity / transferase activity
Similarity search - Function
Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Chem-9F3 / Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsYu, S.H. / Shen, H. / Li, X. / Mu, W.M.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue
Authors: Yu, S.H. / Shen, H. / Cheng, Y.Y. / Zhu, Y.Y. / Li, X. / Mu, W.M.
History
DepositionMar 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DFA-IIIase C387A mutant
B: DFA-IIIase C387A mutant
C: DFA-IIIase C387A mutant
D: DFA-IIIase C387A mutant
E: DFA-IIIase C387A mutant
F: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,94112
Polymers282,9956
Non-polymers1,9466
Water35,6881981
1
A: DFA-IIIase C387A mutant
B: DFA-IIIase C387A mutant
D: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4716
Polymers141,4983
Non-polymers9733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-73 kcal/mol
Surface area36140 Å2
MethodPISA
2
C: DFA-IIIase C387A mutant
E: DFA-IIIase C387A mutant
F: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4716
Polymers141,4983
Non-polymers9733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-71 kcal/mol
Surface area36060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.408, 79.437, 141.009
Angle α, β, γ (deg.)90.00, 100.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DFA-IIIase C387A mutant / difructose anhydride hydrolase / Inulin fructotransferase (DFA-I-forming)


Mass: 47165.891 Da / Num. of mol.: 6 / Mutation: C387A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter chlorophenolicus A6 (bacteria)
Gene: Achl_2895
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B8HDZ1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-9F3 / (2R,3'S,4'S,4aR,5'R,6R,7R,7aS)-4a,5',6-tris(hydroxymethyl)spiro[3,6,7,7a-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane ]-3',4',7-triol / Beta-2,1'-alpha-2',3-Difructofuranose anhydride


Mass: 324.281 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H20O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1981 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 0.1M Sodium malonate (pH 4.2)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 263544 / % possible obs: 95 % / Redundancy: 6.7 % / Net I/σ(I): 16.6
Reflection shellResolution: 1.7→1.73 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.701 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 13158 5 %RANDOM
Rwork0.13148 ---
obs0.1336 250365 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å2-0.61 Å2
2--1.88 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19678 0 132 1981 21791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01920252
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218574
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.93727637
X-RAY DIFFRACTIONr_angle_other_deg1.0033.00342595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.152616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74224.185951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.195152901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.20415132
X-RAY DIFFRACTIONr_chiral_restr0.0910.23142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02123637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024775
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_it1.2741.61410503
X-RAY DIFFRACTIONr_mcbond_other1.2721.61410496
X-RAY DIFFRACTIONr_mcangle_it1.6122.4213102
X-RAY DIFFRACTIONr_mcangle_other1.6132.4213103
X-RAY DIFFRACTIONr_scbond_it1.5881.7929749
X-RAY DIFFRACTIONr_scbond_other1.5881.7929750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9062.62214536
X-RAY DIFFRACTIONr_long_range_B_refined2.94914.24523566
X-RAY DIFFRACTIONr_long_range_B_other2.94914.24623567
X-RAY DIFFRACTIONr_rigid_bond_restr1.598338826
X-RAY DIFFRACTIONr_sphericity_free24.2495477
X-RAY DIFFRACTIONr_sphericity_bonded6.482539892
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 858 -
Rwork0.155 16946 -
obs--86.54 %

+
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