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- PDB-2oqe: Crystal Structure of Hansenula polymorpha amine oxidase in comple... -

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Basic information

Entry
Database: PDB / ID: 2oqe
TitleCrystal Structure of Hansenula polymorpha amine oxidase in complex with Xe to 1.6 Angstroms
Components(Peroxisomal copper amine ...) x 2
KeywordsOXIDOREDUCTASE / protein-derived cofactor / TPQ / Xe / xenon complex
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 / XENON / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJohnson, B.J. / Wilmot, C.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase
Authors: Johnson, B.J. / Cohen, J. / Welford, R.W. / Pearson, A.R. / Schulten, K. / Klinman, J.P. / Wilmot, C.M.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_ref_seq_dif
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Remark 999 SEQUENCE The author states that there is radiation damage at MET634 in the protein that is an ... SEQUENCE The author states that there is radiation damage at MET634 in the protein that is an oxidation clearly visible in chains A and B, but not in chains C,D,E, or F. The protein that went into the crystallization had an unmodified MET at position 634.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal copper amine oxidase
B: Peroxisomal copper amine oxidase
C: Peroxisomal copper amine oxidase
D: Peroxisomal copper amine oxidase
E: Peroxisomal copper amine oxidase
F: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,44685
Polymers444,4016
Non-polymers8,04579
Water68,5293804
1
A: Peroxisomal copper amine oxidase
B: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,17432
Polymers148,1552
Non-polymers3,01930
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peroxisomal copper amine oxidase
D: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,40524
Polymers148,1232
Non-polymers2,28322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Peroxisomal copper amine oxidase
F: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,86629
Polymers148,1232
Non-polymers2,74327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Peroxisomal copper amine oxidase
B: Peroxisomal copper amine oxidase
hetero molecules

E: Peroxisomal copper amine oxidase
F: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,04061
Polymers296,2784
Non-polymers5,76257
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area62310 Å2
ΔGint-309 kcal/mol
Surface area127790 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.403, 222.751, 103.651
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. The asymmetric unit contains three dimers.

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Components

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Peroxisomal copper amine ... , 2 types, 6 molecules ABCDEF

#1: Protein Peroxisomal copper amine oxidase / Methylamine oxidase


Mass: 74077.438 Da / Num. of mol.: 2 / Fragment: residues 13-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: AMO / Plasmid: pDB20 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): CG379 / References: UniProt: P12807, EC: 1.4.3.6
#2: Protein
Peroxisomal copper amine oxidase / Methylamine oxidase


Mass: 74061.438 Da / Num. of mol.: 4 / Fragment: residues 13-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: AMO / Plasmid: pDB20 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): CG379 / References: UniProt: P12807, EC: 1.4.3.6

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Non-polymers , 4 types, 3883 molecules

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


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Chemical...
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Xe
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3804 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / pH: 6
Details: 8% PEG 8000, 0.3M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 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: 1.6→99 Å / Num. obs: 587360 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.373 / % possible all: 72.9

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Phasing

Phasing MRRfactor: 0.328 / Cor.coef. Fo:Fc: 0.694
Highest resolutionLowest resolution
Rotation4 Å48.97 Å
Translation4 Å48.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A2V

1a2v


Resolution: 1.6→46.68 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.484 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. An occupancy greater than 1.0 of atom O4 on residue 405 was used to correctly model a water that is at this position when the cofactor is ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. An occupancy greater than 1.0 of atom O4 on residue 405 was used to correctly model a water that is at this position when the cofactor is in the alternate conformer. This was required because refmac did not refine a 0.5 occupancy water and 0.5 occupancy O4 in an identical position correctly. This problem will exist at the O4 of residue 405 in chains C,D,E and F.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 29665 5.1 %RANDOM
Rwork0.162 ---
obs0.163 587352 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31206 0 324 3804 35334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02232863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.96444759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62854084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35523.7591519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.284155232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3715204
X-RAY DIFFRACTIONr_chiral_restr0.0960.24747
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.215866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.222223
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.23470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.641.519999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.204232563
X-RAY DIFFRACTIONr_scbond_it1.984313499
X-RAY DIFFRACTIONr_scangle_it3.2274.512121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 1585 -
Rwork0.271 29591 -
obs--69.6 %

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