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- PDB-2yg7: Structure-based redesign of cofactor binding in Putrescine Oxidas... -

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Basic information

Entry
Database: PDB / ID: 2yg7
TitleStructure-based redesign of cofactor binding in Putrescine Oxidase: A394C-A396T-Q431G Triple mutant
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 / : / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / 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 / : / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / 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: 2.75 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_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTRESCINE OXIDASE
B: PUTRESCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3474
Polymers98,7762
Non-polymers1,5712
Water72140
1
A: PUTRESCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1742
Polymers49,3881
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTRESCINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1742
Polymers49,3881
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.010, 120.390, 171.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: FAD / End label comp-ID: FAD / Refine code: 1 / Auth seq-ID: 2 - 600 / Label seq-ID: 2

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

#1: Protein PUTRESCINE OXIDASE


Mass: 49387.980 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 394 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 396 TO THR ...ENGINEERED RESIDUE IN CHAIN A, ALA 394 TO CYS ENGINEERED RESIDUE IN CHAIN A, ALA 396 TO THR ENGINEERED RESIDUE IN CHAIN A, GLN 431 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 394 TO CYS ENGINEERED RESIDUE IN CHAIN B, ALA 396 TO THR ENGINEERED RESIDUE IN CHAIN B, GLN 431 TO GLY
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: 2.98 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.4 / Details: pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 31023 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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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 2YG3

2yg3


Resolution: 2.75→98.52 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.84 / SU B: 33.62 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 1.59 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27626 1564 5.1 %RANDOM
Rwork0.23032 ---
obs0.23262 29389 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.702 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--0.96 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.75→98.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 106 40 7054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9679757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88123.653334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.569151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2671560
X-RAY DIFFRACTIONr_chiral_restr0.0920.21071
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_it0.7481.54457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53527126
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32832714
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1364.52630
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: 3504 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
1Atight thermal0.120.5
2Btight thermal0.120.5
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 119 -
Rwork0.356 2153 -
obs--100 %

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