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- PDB-4udp: Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in th... -

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Basic information

Entry
Database: PDB / ID: 4udp
TitleCrystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state
ComponentsGLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / ENZYME / OXIDASE / BIOCATALYSIS / PROTEIN ENGINEERING
Function / homology
Function and homology information


5-(hydroxymethyl)furfural oxidase / Oxidoreductases; Acting on a sulfur group of donors; With oxygen as acceptor / oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / FAD binding
Similarity search - Function
Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5-(hydroxymethyl)furfural oxidase
Similarity search - Component
Biological speciesMethylovorus sp. MP688 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDijkman, W. / Binda, C. / Fraaije, M. / Mattevi, A.
CitationJournal: Acs Catalysis / Year: 2015
Title: Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase
Authors: Dijkman, W.P. / Binda, C. / Fraaije, M.W. / Mattevi, A.
History
DepositionDec 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Dec 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE
B: GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7234
Polymers114,1522
Non-polymers1,5712
Water6,197344
1
A: GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8622
Polymers57,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8622
Polymers57,0761
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.964, 120.907, 72.322
Angle α, β, γ (deg.)90.00, 91.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9937, -0.09548, 0.05934), (-0.09801, -0.9943, 0.04139), (0.05505, -0.04695, -0.9974)
Vector: 0.1465, 78.94, 107.7)

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Components

#1: Protein GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE / 5- HYDROXYMETHYLFURFURAL OXIDASE


Mass: 57076.109 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylovorus sp. MP688 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4QP00
#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.: 344 / 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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growDetails: 16-22% W/V PEG3350, 200 MM MAGNESIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67679 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 0.85 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBV

2jbv


Resolution: 1.9→72.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.939 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23609 3218 4.8 %RANDOM
Rwork0.17805 ---
obs0.18076 64121 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å2-0 Å2-0.11 Å2
2---0.9 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7861 0 106 344 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198168
X-RAY DIFFRACTIONr_bond_other_d0.0020.027717
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9811168
X-RAY DIFFRACTIONr_angle_other_deg0.915317684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21451027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91522.893356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.917151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0841576
X-RAY DIFFRACTIONr_chiral_restr0.1140.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021870
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_it1.8532.3144123
X-RAY DIFFRACTIONr_mcbond_other1.8532.3134122
X-RAY DIFFRACTIONr_mcangle_it2.6483.4615145
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.442.6124045
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 228 -
Rwork0.25 4697 -
obs--99.6 %

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