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- PDB-1a2v: COPPER AMINE OXIDASE FROM HANSENULA POLYMORPHA -

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Basic information

Entry
Database: PDB / ID: 1a2v
TitleCOPPER AMINE OXIDASE FROM HANSENULA POLYMORPHA
ComponentsMETHYLAMINE OXIDASE
KeywordsAMINE OXIDASE / QUINOPROTEIN / TOPAQUINONE ENZYME / 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 / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, SIR / Resolution: 2.4 Å
AuthorsLi, R. / Mathews, F.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallographic study of yeast copper amine oxidase.
Authors: Li, R. / Chen, L. / Cai, D. / Klinman, J.P. / Mathews, F.S.
History
DepositionJan 12, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_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_ref_seq_dif.details / _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: METHYLAMINE OXIDASE
B: METHYLAMINE OXIDASE
C: METHYLAMINE OXIDASE
D: METHYLAMINE OXIDASE
E: METHYLAMINE OXIDASE
F: METHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,52212
Polymers442,1406
Non-polymers3816
Water46,0462556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48050 Å2
ΔGint-309 kcal/mol
Surface area126860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.770, 148.220, 234.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999698, -0.024259, 0.003835), (-0.0236, 0.905602, -0.423471), (0.0068, -0.423434, -0.905901)71.6218, -0.1083, -4.45
2given(0.999774, 0.01863, -0.010253), (0.018234, -0.502964, 0.864115), (0.010941, -0.864106, -0.50319)-0.7217, 70.1706, 17.7194
3given(-0.999871, -0.008885, -0.013382), (-0.012569, -0.085992, 0.996217), (-0.010002, 0.996256, 0.085869)70.7667, 55.8633, -50.1406
4given(0.999715, 0.018202, 0.015433), (0.022436, -0.496556, -0.867715), (-0.008131, 0.867814, -0.496823)-0.4454, 50.0655, -51.5361
5given(-0.999992, -0.001028, 0.003802), (-0.001343, -0.818552, -0.574431), (0.003703, -0.574432, 0.818544)70.6447, 67.2305, 21.1011

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Components

#1: Protein
METHYLAMINE OXIDASE


Mass: 73690.047 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12807, EC: 1.4.3.6
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2556 / 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: 2.6 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.2
Details: PROTEIN WAS CRYSTALLIZED IN SITTING DROPS FROM 7-9% PEG 8000 AND 0.3 M POTASSIUM PHOSPHATE BUFFER, PH 6.2
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
2155 mMpotassium phosphate1drop
33.5-4.5 %PEG80001drop
40.3 Mpotassium phosphate1reservoir
57-9 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 172832 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.247 / % possible all: 66.8
Reflection shell
*PLUS
% possible obs: 66.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEITdata reduction
X-PLOR3.843model building
X-PLOR3.843refinement
SCALEITdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SIR
Starting model: PDB ENTRY 1OAC

1oac


Resolution: 2.4→100 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: BULK SOLVENT MODEL USED NCS RESTRAINTS. GROUP 1 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 1 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 1 B- ...Details: BULK SOLVENT MODEL USED NCS RESTRAINTS. GROUP 1 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 1 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 1 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 2 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 2 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 2 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 2 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 3 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 3 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 3 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 3 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 4 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 4 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 4 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 4 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 5 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 5 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 5 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 5 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 6 POSITIONAL MAIN CHAIN (KCAL/MOL-A**2) : 15 GROUP 6 B-FACTOR MAIN CHAIN (A**2) : 4 GROUP 6 POSITIONAL SIDE CHAIN (KCAL/MOL-A**2) : 10 GROUP 6 B-FACTOR MAIN CHAIN (A**2) : 4
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7906 5 %RANDOM
Rwork0.184 ---
obs0.184 157428 83.6 %-
Displacement parametersBiso mean: 24.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31164 0 6 2556 33726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.381.5
X-RAY DIFFRACTIONx_mcangle_it3.452
X-RAY DIFFRACTIONx_scbond_it3.92
X-RAY DIFFRACTIONx_scangle_it5.382.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 834 5.1 %
Rwork0.279 15638 -
obs--53.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAMPARAM:TOPOLOGY.YAO
X-RAY DIFFRACTION3PARAM:PARAM_YAO.SOL
X-RAY DIFFRACTION4PARAM:PARAM.TPQ
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor obs: 0.279

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