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- PDB-3rja: Crystal structure of carbohydrate oxidase from Microdochium nival... -

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Basic information

Entry
Database: PDB / ID: 3rja
TitleCrystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue
ComponentsCarbohydrate oxidase
KeywordsOXIDOREDUCTASE / protein-substrate analogue complex / FAD binding domain / berberine and berberine-like domain / glucooligosaccharide oxidase / FAD Binding / Carbohydrate/Sugar Binding / extracellular
Function / homology
Function and homology information


hexose oxidase / glucose oxidase activity / Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / FAD binding / extracellular region / metal ion binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ABL / FLAVIN-ADENINE DINUCLEOTIDE / Carbohydrate oxidase
Similarity search - Component
Biological speciesMicrodochium nivale (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDuskova, J. / Skalova, T. / Kolenko, P. / Stepankova, A. / Koval, T. / Hasek, J. / Ostergaard, L.H. / Fuglsang, C.C. / Dohnalek, J.
Citation
Journal: To be Published
Title: Crystal structure and kinetic studies of carbohydrate oxidase from Microdochium nivale
Authors: Duskova, J. / Skalova, T. / Kolenko, P. / Stepankova, A. / Hasek, J. / Koval, T. / Ostergaard, L.H. / Fuglsang, C.C. / Dohnalek, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization of carbohydrate oxidase from Microdochium nivale.
Authors: Duskova, J. / Dohnalek, J. / Skalova, T. / Ostergaard, L.H. / Fuglsang, C.C. / Kolenko, P. / Stepankova, A. / Hasek, J.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 22, 2023Group: Database references / Structure summary / Category: chem_comp / database_2 / entity
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec
Revision 2.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,70914
Polymers52,4671
Non-polymers2,24213
Water11,043613
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.040, 56.920, 86.900
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-602-

ZN

21A-603-

ZN

31A-616-

HOH

41A-704-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbohydrate oxidase


Mass: 52466.957 Da / Num. of mol.: 1 / Fragment: mature enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microdochium nivale (fungus) / Strain: NN008551 / Gene: MnCO / Plasmid: pEJG33 / Production host: Aspergillus oryzae (mold) / Strain (production host): JaL228 / References: UniProt: I1SB12*PLUS, hexose oxidase

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Sugars , 2 types, 3 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-ABL / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside / 5-amino-5-deoxy-cellobiono-1,5-lactam / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl glucoside


Type: D-saccharide / Mass: 339.296 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H21NO10
IdentifierTypeProgram
5-amino-5-deoxy-cellobiono-1,5-lactamIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 623 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M zinc sulfate, 0.1 M MES, 12% PEG550 MME , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418
DetectorType: Oxford Diffraction Atlas CCD / Detector: CCD / Date: Jun 5, 2008 / Details: Enhance Ultra
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 33917 / Num. obs: 33917 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -100 / Redundancy: 2.2 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4312 / % possible all: 63.1

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.6.0060refinement
CrysalisProdata reduction
Jana2006data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZR6

1zr6


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.961 / SU B: 2.542 / SU ML: 0.068 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / ESU R: 0.17
Stereochemistry target values: CCP4 6.1.3 stereochemistry library
Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.202 (FREE R = 0.284 FOR THE HIGHEST RESOLUTION SHELL) FROM A RANDOM TEST SET ...Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.202 (FREE R = 0.284 FOR THE HIGHEST RESOLUTION SHELL) FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (1694 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflection
Rwork0.142 --
obs0.145 33917 90.11 %
all-33917 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-1.4 Å2
2---0.54 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 133 613 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9745545
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79123.587184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75415610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7081522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213110
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.173 1498 -
obs-1498 55.52 %

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