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- PDB-3sx1: Hansenula polymorpha copper amine oxidase-1 in its apo form -

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Basic information

Entry
Database: PDB / ID: 3sx1
TitleHansenula polymorpha copper amine oxidase-1 in its apo form
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / peroxisome
Function / homology
Function and homology information


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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKlema, V.J. / Johnson, B.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 14, 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,28218
Polymers232,8983
Non-polymers1,38415
Water46,5512584
1
A: Peroxisomal primary amine oxidase
hetero molecules

A: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,37014
Polymers155,2652
Non-polymers1,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13760 Å2
ΔGint-58 kcal/mol
Surface area44130 Å2
MethodPISA
2
B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,09711
Polymers155,2652
Non-polymers8329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-63 kcal/mol
Surface area44680 Å2
MethodPISA
3
A: Peroxisomal primary amine oxidase
hetero molecules

A: Peroxisomal primary amine oxidase
hetero molecules

B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules

B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,56436
Polymers465,7966
Non-polymers2,76930
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_445-x-1/2,y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area47020 Å2
ΔGint-221 kcal/mol
Surface area127600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.617, 153.636, 223.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-912-

HOH

21B-1183-

HOH

31B-1521-

HOH

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Components

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


Mass: 77632.617 Da / Num. of mol.: 3
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 2584 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG 8000, 0.28 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 247478 / Num. obs: 240796 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.074 / Net I/σ(I): 32.3
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.447 / % possible all: 88.1

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Processing

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

2oov


Resolution: 1.73→31.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.133 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 12085 5 %RANDOM
Rwork0.13205 ---
obs0.13359 228647 97.4 %-
all-234751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.719 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15596 0 89 2584 18269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216499
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.95822533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80652096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49823.789768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.738152669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51215101
X-RAY DIFFRACTIONr_chiral_restr0.1470.22401
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02112855
X-RAY DIFFRACTIONr_mcbond_it1.5271.510065
X-RAY DIFFRACTIONr_mcangle_it2.493216424
X-RAY DIFFRACTIONr_scbond_it3.94936434
X-RAY DIFFRACTIONr_scangle_it6.1384.56044
LS refinement shellResolution: 1.732→1.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 869 -
Rwork0.202 15773 -
obs--92.1 %
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)
10.0290.0015-0.02510.0112-0.00470.1016-0.01760.00510.0004-0.00050.003-0.00180.0359-0.00430.01450.0167-0.00420.00620.0055-0.00460.0094-1.1887-3.399138.2791
20.0182-0.0145-0.02060.06810.02830.08170.0125-0.00380.0003-0.0217-0.0073-0.0031-0.027-0.0113-0.00520.01340.00190.00320.0060.0010.0053-68.6292-5.874228.8479
30.02230.01410.00610.1540.03780.0225-0.0009-0.0027-0.0081-0.03950.0054-0.025-0.0118-0.0008-0.00460.0127-0.00510.00660.0085-0.00320.0072-54.5924-35.0915.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 672
2X-RAY DIFFRACTION1A693 - 698
3X-RAY DIFFRACTION1A699 - 3000
4X-RAY DIFFRACTION2B16 - 672
5X-RAY DIFFRACTION2B693 - 697
6X-RAY DIFFRACTION2B698 - 3003
7X-RAY DIFFRACTION3C16 - 671
8X-RAY DIFFRACTION3C693 - 696
9X-RAY DIFFRACTION3C697 - 3004

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