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- PDB-4a7z: Complex of bifunctional aldos-2-ulose dehydratase with the reacti... -

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Basic information

Entry
Database: PDB / ID: 4a7z
TitleComplex of bifunctional aldos-2-ulose dehydratase with the reaction intermediate ascopyrone M
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
Ascopyrone M / Aldos-2-ulose dehydratase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.1Jan 16, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf ..._chem_comp.type / _pdbx_database_status.status_code_sf / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,3617
Polymers98,8521
Non-polymers5096
Water3,405189
1
A: ALDOS-2-ULOSE DEHYDRATASE
hetero molecules

A: ALDOS-2-ULOSE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,72214
Polymers197,7052
Non-polymers1,01812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area6100 Å2
ΔGint-122.2 kcal/mol
Surface area67530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.220, 82.670, 97.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 3 / 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-AY9 / Ascopyrone M


Type: D-saccharide / Mass: 144.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BISTRIS-PROPANE, 0.2 M NACL, 16% PEG6000. CRYSTALS WERE OBTAINED BY CO-CRYSTALLISATION IN THE PRESENCE OF 0.2 M ANHYDROFRUCTOSE INCUBATED WITH 0,2M HYDROXYLAMINE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.6→42 Å / Num. obs: 33047 / % possible obs: 93.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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Processing

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

4a7k


Resolution: 2.6→41.33 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.865 / SU B: 22.385 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.758 / ESU R Free: 0.337 / 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
Rfree0.26694 1674 5.1 %RANDOM
Rwork0.19376 ---
obs0.19739 31351 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6801 0 24 189 7014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9429612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1935881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65523.407317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.982151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1891548
X-RAY DIFFRACTIONr_chiral_restr0.1070.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215529
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 103 -
Rwork0.305 2150 -
obs--99.08 %
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)
12.20540.7484-1.30541.0826-0.51432.35270.118-0.33390.02880.083-0.16750.0232-0.18680.33660.04950.1489-0.03110.0010.06590.00920.2021-24.403-43.05360.449
21.03940.1373-0.16970.94660.33021.2249-0.03910.14860.1859-0.08380.0614-0.0108-0.15730.0667-0.02230.1685-0.0212-0.02450.02860.03060.2145-0.992-22.7722.632
33.27240.30680.91793.1652-0.61333.435-0.11530.56910.1332-0.17860.25230.64120.0259-0.564-0.1370.2121-0.0963-0.07540.30020.0970.3379-27.083-41.1193.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 433
2X-RAY DIFFRACTION1A950 - 951
3X-RAY DIFFRACTION1A953 - 954
4X-RAY DIFFRACTION2A434 - 739
5X-RAY DIFFRACTION2A952
6X-RAY DIFFRACTION2A955
7X-RAY DIFFRACTION3A740 - 900

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