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- PDB-2wdw: The Native Crystal Structure of the Primary Hexose Oxidase (Dbv29... -

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Basic information

Entry
Database: PDB / ID: 2wdw
TitleThe Native Crystal Structure of the Primary Hexose Oxidase (Dbv29) in Antibiotic A40926 Biosynthesis
ComponentsPUTATIVE HEXOSE OXIDASE
KeywordsOXIDOREDUCTASE / FAD / FLAVOPROTEIN / HEXOSE OXIDASE
Function / homology
Function and homology information


acyltransferase activity / glycosyltransferase activity / FAD binding / monooxygenase activity
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 ...: / 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
FLAVIN-ADENINE DINUCLEOTIDE / Putative hexose oxidase
Similarity search - Component
Biological speciesNONOMURAEA SP. ATCC 39727 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLiu, Y.-C. / Li, Y.-S. / Lyu, S.-Y. / Chen, Y.-H. / Chan, H.-C. / Huang, C.-J. / Huang, Y.-T. / Chen, G.-H. / Chou, C.-C. / Tsai, M.-D. / Li, T.-L.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Interception of Teicoplanin Oxidation Intermediates Yields New Antimicrobial Scaffolds
Authors: Liu, Y.-C. / Li, Y.-S. / Lyu, S.-Y. / Hsu, L.-J. / Chen, Y.-H. / Huang, Y.-T. / Chan, H.-C. / Huang, C.-J. / Chen, G.-H. / Chou, C.-C. / Tsai, M.-D. / Li, T.-L.
History
DepositionMar 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE HEXOSE OXIDASE
B: PUTATIVE HEXOSE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6894
Polymers114,1182
Non-polymers1,5712
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36.3 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.092, 66.092, 790.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PUTATIVE HEXOSE OXIDASE / PRIMARY HEXOSE OXIDASE


Mass: 57059.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NONOMURAEA SP. ATCC 39727 (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q7WZ62, alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.81 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 550 MME, 0.05M CALCIUM CHLORIDE, 0.1M BIS TRIS, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9731
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9731 Å / Relative weight: 1
ReflectionResolution: 3.21→30 Å / Num. obs: 17824 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8
Reflection shellResolution: 3.21→3.32 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 17 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IPI

2ipi


Resolution: 3.21→29.54 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.83 / SU B: 27.218 / SU ML: 0.458 / Cross valid method: THROUGHOUT / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 869 4.9 %RANDOM
Rwork0.237 ---
obs0.24 16838 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 3.21→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7710 0 106 67 7883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0228049
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8371.96911004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1795994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18823.26362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.981562
X-RAY DIFFRACTIONr_chiral_restr0.0530.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026316
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1520.23884
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25386
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1251.55048
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.22527972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.16333489
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2954.53032
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: 3.21→3.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 57 -
Rwork0.274 1170 -
obs--92.39 %

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