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- PDB-3loy: Crystal structure of a Copper-containing benzylamine oxidase from... -

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Basic information

Entry
Database: PDB / ID: 3loy
TitleCrystal structure of a Copper-containing benzylamine oxidase from Hansenula Polymorpha
Componentscopper amine oxidase
KeywordsOXIDOREDUCTASE / amine oxidase / TPQ
Function / homology
Function and homology information


Copper amine oxidase, catalytic domain / Nuclear Transport Factor 2; Chain: A, - #40 / 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 / L(+)-TARTARIC ACID / :
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlema, V.J. / Johnson, B.J. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2010
Title: Kinetic and structural analysis of substrate specificity in two copper amine oxidases from Hansenula polymorpha.
Authors: Chang, C.M. / Klema, V.J. / Johnson, B.J. / Mure, M. / Klinman, J.P. / Wilmot, C.M.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_special_symmetry / 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_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_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.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_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: copper amine oxidase
B: copper amine oxidase
C: copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,16620
Polymers216,5673
Non-polymers1,59917
Water57,5583195
1
A: copper amine oxidase
B: copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,48714
Polymers144,3782
Non-polymers1,10912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-104 kcal/mol
Surface area41810 Å2
MethodPISA
2
C: copper amine oxidase
hetero molecules

C: copper amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,35812
Polymers144,3782
Non-polymers98010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area15300 Å2
ΔGint-94 kcal/mol
Surface area41560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)288.510, 91.065, 151.098
Angle α, β, γ (deg.)90.00, 117.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1952-

HOH

21C-2738-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein copper amine oxidase


Mass: 72189.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: E7R5K2*PLUS, primary-amine oxidase

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Non-polymers , 5 types, 3212 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3195 / 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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.55M potassium sodium tartrate tetrahydrate in 0.10M phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Aug 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 200161 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.382
Reflection shellResolution: 2→2.057 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3 / Num. unique all: 10684 / % possible all: 65.72

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OOV

2oov


Resolution: 2→37.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.082 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: NO ELECTRON DENSITY FOR THE CARBOXYLIC HEAD GROUP OF ASP585 WAS SEEN DUE TO RADIATION DAMAGE, SO THIS RESIDUE HAS BEEN MODELED AS AN ALANINE IN ALL THREE PROTEIN CHAINS. HYDROGENS HAVE BEEN ...Details: NO ELECTRON DENSITY FOR THE CARBOXYLIC HEAD GROUP OF ASP585 WAS SEEN DUE TO RADIATION DAMAGE, SO THIS RESIDUE HAS BEEN MODELED AS AN ALANINE IN ALL THREE PROTEIN CHAINS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19079 10514 5 %RANDOM
Rwork0.1447 ---
obs0.147 200161 90.4 %-
all-233058 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.01 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15243 0 94 3195 18532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02215825
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.96121543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49651916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89423.979754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.949152592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.72915101
X-RAY DIFFRACTIONr_chiral_restr0.2030.22339
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112209
X-RAY DIFFRACTIONr_mcbond_it1.1841.59564
X-RAY DIFFRACTIONr_mcangle_it1.987215639
X-RAY DIFFRACTIONr_scbond_it3.48236261
X-RAY DIFFRACTIONr_scangle_it5.2094.55894
LS refinement shellResolution: 2→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 539 -
Rwork0.219 11223 -
obs-10684 65.72 %

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