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- PDB-4kff: Crystal structure of Hansenula polymorpha copper amine oxidase-1 ... -

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Basic information

Entry
Database: PDB / ID: 4kff
TitleCrystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 8.5
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / amine oxidase / peroxisome
Function / homology
Function and homology information


primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / peroxisome / copper ion binding
Similarity search - Function
Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 ...Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesOgataea angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJohnson, B.J. / Yukl, E.T. / Klema, V.J. / Wilmot, C.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural evidence for the semiquinone in a copper amine oxidase from Hansenula polymorpha: implications for the catalytic mechanism
Authors: Johnson, B.J. / Yukl, E.T. / Klema, V.J. / Klinman, J.P. / Wilmot, C.M.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal primary amine oxidase
B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,46520
Polymers232,9853
Non-polymers1,48017
Water22,3931243
1
A: Peroxisomal primary amine oxidase
hetero molecules

A: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,74018
Polymers155,3232
Non-polymers1,41616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17010 Å2
ΔGint-55 kcal/mol
Surface area43880 Å2
MethodPISA
2
B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,09511
Polymers155,3232
Non-polymers7729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-65 kcal/mol
Surface area44430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.022, 153.316, 223.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1099-

HOH

21A-1222-

HOH

31B-936-

HOH

41B-1017-

HOH

51B-1067-

HOH

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Components

#1: Protein Peroxisomal primary amine oxidase / Copper amine oxidase / Methylamine oxidase


Mass: 77661.617 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ogataea angusta (fungus) / Gene: AMO / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12807, primary-amine oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1243 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 8.0-9.5% PEG8000, 0.28-0.30 M phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2005
RadiationMonochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 122479 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.19 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOV

2oov


Resolution: 2.15→38.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.727 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 6492 5 %RANDOM
Rwork0.142 ---
obs0.144 122479 99.9 %-
all-239867 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15602 0 87 1243 16932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916202
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214979
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9622061
X-RAY DIFFRACTIONr_angle_other_deg0.868334603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53851987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48423.785753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.663152554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7111599
X-RAY DIFFRACTIONr_chiral_restr0.1150.22350
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023748
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.15→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 462 -
Rwork0.173 8925 -
obs--99.03 %

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