[English] 日本語
Yorodumi
- PDB-4a7y: Active site metal depleted aldos-2-ulose dehydratase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a7y
TitleActive site metal depleted aldos-2-ulose dehydratase
ComponentsALDOS-2-ULOSE DEHYDRATASE
KeywordsLYASE / DEHYDRATASE/ISOMERASE / LIGNIN DEGRADATION / CORTALCERONE/MICROTHECIN FORMING / METALLOENZYME
Function / homology
Function and homology information


aldos-2-ulose dehydratase / aldos-2-ulose dehydratase activity / 1,5-anhydro-D-fructose dehydratase activity / hydro-lyase activity / isomerase activity / metal ion binding
Similarity search - Function
Jelly Rolls - #990 / Aldos-2-ulose dehydratase/isomerase (AUDH), Cupin domain / : / : / Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain / Aldos-2-ulose dehydratase, beta-propeller domain / Integrin alpha, N-terminal / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...Jelly Rolls - #990 / Aldos-2-ulose dehydratase/isomerase (AUDH), Cupin domain / : / : / Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain / Aldos-2-ulose dehydratase, beta-propeller domain / Integrin alpha, N-terminal / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,5-anhydro-D-fructose / Aldos-2-ulose dehydratase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsClaesson, M. / Lindqvist, Y. / Madrid, S. / Sandalova, T. / Fiskesund, R. / Yu, S. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of Bifunctional Aldos-2-Ulose Dehydratase/Isomerase from Phanerochaete Chrysosporium with the Reaction Intermediate Ascopyrone M.
Authors: Claesson, M. / Lindqvist, Y. / Madrid, S. / Sandalova, T. / Fiskesund, R. / Yu, S. / Schneider, G.
History
DepositionNov 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALDOS-2-ULOSE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2665
Polymers98,8521
Non-polymers4144
Water1,11762
1
A: ALDOS-2-ULOSE DEHYDRATASE
hetero molecules

A: ALDOS-2-ULOSE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,53310
Polymers197,7052
Non-polymers8288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area7100 Å2
ΔGint-56.5 kcal/mol
Surface area67810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.410, 82.240, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein ALDOS-2-ULOSE DEHYDRATASE / D-ARABINO-HEX-2-ULOSE DEHYDRATASE / PYRANOSONE DEHYDRATASE


Mass: 98852.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Production host: OGATAEA ANGUSTA (fungus) / Strain (production host): RB11(URA-) / References: UniProt: P84193, aldos-2-ulose dehydratase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-NHF / 1,5-anhydro-D-fructose


Type: D-saccharide / Mass: 162.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.69 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BISTRIS-PROPANE BUFFER, PH 7, 0.2 M NACL, 10% PEG6000. THE CRYSTALS WERE SOAKED IN 10MM ANHYDROFRUCTOSE BEFORE DATA COLLECTION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.28
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.8→70 Å / Num. obs: 23405 / % possible obs: 88.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A7K

4a7k


Resolution: 2.8→56.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.867 / SU B: 33.643 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1226 5.3 %RANDOM
Rwork0.18344 ---
obs0.18752 22079 86.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.8→56.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 24 62 6882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9429592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48923.407317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.143151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9311548
X-RAY DIFFRACTIONr_chiral_restr0.0950.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215511
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 97 -
Rwork0.303 1555 -
obs--88.53 %
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)
12.04470.6092-0.95011.2962-0.14492.04660.0923-0.23620.05560.0945-0.102-0.0591-0.10710.21230.00970.0819-0.0192-0.00320.03570.00110.0931-24.4105-42.843560.3146
21.22250.0032-0.16261.03240.39111.4107-0.01270.16620.1679-0.11160.0473-0.0013-0.17170.084-0.03460.0546-0.0137-0.01490.03170.02490.066-0.9922-22.663422.3889
32.76270.30190.62043.5687-0.48153.5471-0.06390.44970.0855-0.17110.16170.6612-0.0073-0.5377-0.09780.139-0.058-0.05560.24780.05070.1931-27.1966-40.93733.3677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 433
2X-RAY DIFFRACTION1A951 - 952
3X-RAY DIFFRACTION2A434 - 739
4X-RAY DIFFRACTION2A953 - 954
5X-RAY DIFFRACTION3A740 - 900

+
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