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

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Basic information

Entry
Database: PDB / ID: 4kfe
TitleCrystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 7.0
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / amine oxidase / peroxisome
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / 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 / FORMYL GROUP / HYDROGEN PEROXIDE / PHOSPHATE ION / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesOgataea angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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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
D: Peroxisomal primary amine oxidase
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,71976
Polymers465,9706
Non-polymers5,74970
Water78,9964385
1
A: Peroxisomal primary amine oxidase
B: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,69931
Polymers155,3232
Non-polymers2,37629
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-104 kcal/mol
Surface area43290 Å2
MethodPISA
2
C: Peroxisomal primary amine oxidase
D: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,11724
Polymers155,3232
Non-polymers1,79422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-103 kcal/mol
Surface area43740 Å2
MethodPISA
3
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,90321
Polymers155,3232
Non-polymers1,57919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18690 Å2
ΔGint-100 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.577, 222.836, 103.619
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 77661.617 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 4455 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2O2
#4: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4385 / Source method: isolated from a natural source / Formula: H2O

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Details

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 / Method: vapor diffusion, hanging drop / pH: 7
Details: 8.0-9.5% PEG8000, 0.28-0.30 M phosphate, pH 7.0, 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 Å
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: 2.1→50 Å / Num. all: 269552 / Num. obs: 265779 / % possible obs: 98.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3
Reflection shellHighest resolution: 2.1 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.83 / % possible all: 89.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→49.03 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.776 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18033 13290 5 %RANDOM
Rwork0.12896 ---
obs0.13155 252434 98.53 %-
all-269689 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0.09 Å2
2--0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31209 0 351 4385 35945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01932675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0230292
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.96244461
X-RAY DIFFRACTIONr_angle_other_deg0.893369990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45454014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27323.7761507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.467155155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.13415199
X-RAY DIFFRACTIONr_chiral_restr0.1150.24758
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02136989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027528
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 876 -
Rwork0.21 16460 -
obs--87.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01250.02290.00910.12930.01620.0374-0.00480.0025-0.0125-0.02080.0175-0.0265-0.0053-0.0001-0.01270.0080.00030.00560.0084-0.00620.01654.9408-17.7135-1.8244
20.03620.01320.01590.12950.03410.0165-0.0113-0.0013-0.0058-0.02290.0198-0.0212-0.01380.0027-0.00850.0211-0.00720.00690.0089-0.00150.005253.93517.713-2.9463
30.06990.0158-0.07830.0387-0.0180.12210.0243-0.00940.0140.00430.00590.0076-0.03260.0186-0.03020.032-0.00770.00720.0055-0.00420.009230.480640.975639.3996
40.02850.0109-0.01640.12180.02250.0280.0130.00220.00370.0195-0.01460.0371-0.00410.00010.00160.01740.00020.00830.0042-0.00580.0135-0.634126.857348.9726
50.04190.0139-0.02510.11540.0180.03750.0043-0.0003-0.00160.0331-0.01340.023500.00480.00910.0136-0.00520.00870.0052-0.00050.0143-2.2646-26.869147.1672
60.1063-0.015-0.05260.0350.01260.0453-0.02810.0169-0.03610.0050.00640.0060.0072-0.00540.02180.0103-0.00440.00550.0056-0.00740.028810.4371-40.979817.1834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 672
2X-RAY DIFFRACTION1A801 - 803
3X-RAY DIFFRACTION2B15 - 672
4X-RAY DIFFRACTION2B801 - 803
5X-RAY DIFFRACTION3C17 - 672
6X-RAY DIFFRACTION3C801 - 802
7X-RAY DIFFRACTION4D17 - 672
8X-RAY DIFFRACTION4D701 - 702
9X-RAY DIFFRACTION4F801
10X-RAY DIFFRACTION5E17 - 672
11X-RAY DIFFRACTION5E801 - 802
12X-RAY DIFFRACTION6F17 - 672
13X-RAY DIFFRACTION6D703
14X-RAY DIFFRACTION6F802

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