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- PDB-2oov: Crystal Structure of Hansenula polymorpha amine oxidase to 1.7 An... -

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Basic information

Entry
Database: PDB / ID: 2oov
TitleCrystal Structure of Hansenula polymorpha amine oxidase to 1.7 Angstroms
Components(Peroxisomal copper amine ...) x 2
KeywordsOXIDOREDUCTASE / protein-derived cofactor / beta-sandwich / TPQ
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / 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 / Copper amine oxidase, catalytic domain ...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 / PHOSPHATE ION / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 26, 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: Derived calculations / Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2012Group: Derived calculations
Revision 1.4Oct 18, 2017Group: Refinement description / Category: 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 1.5Aug 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 / 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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)447,55042
Polymers444,4016
Non-polymers3,15036
Water91,0665055
1
A: Peroxisomal copper amine oxidase
B: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,38716
Polymers148,1552
Non-polymers1,23214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17350 Å2
ΔGint-96 kcal/mol
Surface area43470 Å2
MethodPISA
2
C: Peroxisomal copper amine oxidase
D: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,89811
Polymers148,1232
Non-polymers7759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15920 Å2
ΔGint-94 kcal/mol
Surface area43950 Å2
MethodPISA
3
E: Peroxisomal copper amine oxidase
F: Peroxisomal copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,26615
Polymers148,1232
Non-polymers1,14313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-98 kcal/mol
Surface area43820 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56430 Å2
ΔGint-322 kcal/mol
Surface area125120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.146, 223.082, 104.248
Angle α, β, γ (deg.)90.000, 95.770, 90.000
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, 5091 molecules

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


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 5055 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG 8000, 0.3M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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 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: 1.7→50 Å / Num. obs: 437335 / % possible obs: 85.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.085 / Χ2: 0.96 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Num. unique all: 18134 / Χ2: 0.706 / % possible all: 35.3

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Phasing

Phasing MRRfactor: 0.301 / Cor.coef. Fo:Fc: 0.736
Highest resolutionLowest resolution
Rotation4 Å40.53 Å
Translation4 Å40.53 Å

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Processing

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

1a2v


Resolution: 1.7→37.96 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.725 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.097
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
Rfree0.178 21965 5 %RANDOM
Rwork0.147 ---
obs0.149 437276 84.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.284 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31166 0 184 5055 36405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02232682
X-RAY DIFFRACTIONr_angle_refined_deg1.331.96144493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02954050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.923.8131516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.164155208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01115199
X-RAY DIFFRACTIONr_chiral_restr0.0970.24728
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225375
X-RAY DIFFRACTIONr_nbd_refined0.1890.216577
X-RAY DIFFRACTIONr_nbtor_refined0.3070.222104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.24765
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.254
X-RAY DIFFRACTIONr_mcbond_it0.6781.520456
X-RAY DIFFRACTIONr_mcangle_it1.037232429
X-RAY DIFFRACTIONr_scbond_it1.744313965
X-RAY DIFFRACTIONr_scangle_it2.7224.511998
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 606 -
Rwork0.226 11620 -
obs-12226 32.14 %

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