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- PDB-3sxx: Hansenula polymorpha copper amine oxidase-1 in complex with Co(II) -

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Basic information

Entry
Database: PDB / ID: 3sxx
TitleHansenula polymorpha copper amine oxidase-1 in complex with Co(II)
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / peroxisome
Function / homology
Function and homology information


aliphatic amine oxidase activity / 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
: / PHOSPHATE ION / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.27 Å
AuthorsKlema, V.J. / Wilmot, C.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: The precursor form of Hansenula polymorpha copper amine oxidase 1 in complex with CuI and CoII.
Authors: Klema, V.J. / Johnson, B.J. / Klinman, J.P. / Wilmot, C.M.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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
D: Peroxisomal primary amine oxidase
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,29957
Polymers465,7966
Non-polymers4,50451
Water112,1436225
1
A: Peroxisomal primary amine oxidase
B: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,04122
Polymers155,2652
Non-polymers1,77620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-66 kcal/mol
Surface area44550 Å2
MethodPISA
2
C: Peroxisomal primary amine oxidase
D: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,67518
Polymers155,2652
Non-polymers1,41016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-69 kcal/mol
Surface area45080 Å2
MethodPISA
3
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,58317
Polymers155,2652
Non-polymers1,31815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-67 kcal/mol
Surface area44810 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49370 Å2
ΔGint-241 kcal/mol
Surface area128550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.887, 223.364, 103.969
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 77632.617 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: AMO / Production host: Escherichia coli (E. coli) / References: UniProt: P12807, primary-amine oxidase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6225 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 298 K / pH: 6
Details: 8.5% PEG 8000, 0.27 M potassium phosphate, pH 6.0, 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: 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2007
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 1169541 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.073 / Net I/σ(I): 23.5
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.357 / % possible all: 85.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ID 2OOV

2oov


Resolution: 1.27→31.7 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.907 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.138 58671 5 %RANDOM
Rwork0.108 ---
obs0.109 1110572 94.9 %-
all-1170625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.06 Å2
2--0.04 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.27→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31402 0 274 6225 37901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02233837
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9646255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85354345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19323.7741587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.813155473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0415215
X-RAY DIFFRACTIONr_chiral_restr0.240.24901
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02126457
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_it2.7441.520567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.761233618
X-RAY DIFFRACTIONr_scbond_it5.477313270
X-RAY DIFFRACTIONr_scangle_it7.4144.512468
X-RAY DIFFRACTIONr_rigid_bond_restr3.105333837
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 3854 -
Rwork0.174 72499 -
obs--84.16 %
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)
10.0001-0.00010.00010.0007-0.00010.0001-0-00.0001-0.0001-0-0.00010.0001-0.00010.00010.002900.00290.0001-0.00010.0032-6.837716.854.941
20.0001-0-00.0007-0.00020.0003-0-0.0001-0-0.00010.0001-00.0001-0-00.0029-0.00010.00290.000100.0031-8.294-17.624753.0671
30.00050.0002-00.0002-0.00020.00030.0001-0.0001-00-0.00010-00.0001-00.003-00.00290.000100.003237.0714-40.225433.8389
40.00030.0001-0.00020.0002-0.00030.00040000.0001-00-0-0-00.002900.00280-00.003248.6543-26.60514.3334
50.0008-0.0004-0.00030.00040.00030.0003-000.000100.0001-000.0001-00.0029-00.00280.000100.003246.774627.12433.0176
60.0003-0.0002-0.00020.00030.00020.0003-00.00010-0-0.00010.0001-0-0.00010.00010.002900.00290.0001-00.003215.898140.677712.0202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 691
2X-RAY DIFFRACTION2B16 - 691
3X-RAY DIFFRACTION3C16 - 691
4X-RAY DIFFRACTION4D16 - 672
5X-RAY DIFFRACTION5E16 - 671
6X-RAY DIFFRACTION6F16 - 691

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