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- PDB-2yg3: Structure-based redesign of cofactor binding in Putrescine Oxidas... -

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Basic information

Entry
Database: PDB / ID: 2yg3
TitleStructure-based redesign of cofactor binding in Putrescine Oxidase: wild type enzyme
ComponentsPUTRESCINE OXIDASE
KeywordsOXIDOREDUCTASE / FLAVIN
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putrescine oxidase
Similarity search - Component
Biological speciesRHODOCOCCUS ERYTHROPOLIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKopacz, M.M. / Rovida, S. / van Duijn, E. / Fraaije, M.W. / Mattevi, A.
CitationJournal: Biochemistry / Year: 2011
Title: Structure-Based Redesign of Cofactor Binding in Putrescine Oxidase.
Authors: Kopacz, M.M. / Rovida, S. / Van Duijn, E. / Fraaije, M.W. / Mattevi, A.
History
DepositionApr 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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: PUTRESCINE OXIDASE
B: PUTRESCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,01811
Polymers98,7942
Non-polymers2,2249
Water17,150952
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-40.6 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.570, 79.770, 91.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 600
2111B1 - 600

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Components

#1: Protein PUTRESCINE OXIDASE


Mass: 49396.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Description: TOP10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: B0F9F6, putrescine 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / 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: 3.66 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.4
Details: 100MM MES PH 6.4, 2.2M AMMONIUM SULFATE, 100MM SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 96941 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5Z

2v5z


Resolution: 2→98.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.772 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20102 4847 5 %RANDOM
Rwork0.17516 ---
obs0.17646 92031 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2→98.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 146 952 8004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9719785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44323.69336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.291151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5381560
X-RAY DIFFRACTIONr_chiral_restr0.0890.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215492
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_it0.5751.54451
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17227112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14432746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6474.52673
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3503 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.160.05
2Btight positional0.160.05
1Atight thermal0.190.5
2Btight thermal0.190.5
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 326 -
Rwork0.223 6487 -
obs--95.27 %

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