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- PDB-1ekm: CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER ... -

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Basic information

Entry
Database: PDB / ID: 1ekm
TitleCRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI
ComponentsCOPPER AMINE OXIDASE
KeywordsOXIDOREDUCTASE / amine oxidase / quinoprotein
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
Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsChen, Z. / Schwartz, B. / Williams, N.K. / Li, R. / Klinman, J.P. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal structure at 2.5 A resolution of zinc-substituted copper amine oxidase of Hansenula polymorpha expressed in Escherichia coli.
Authors: Chen, Z. / Schwartz, B. / Williams, N.K. / Li, R. / Klinman, J.P. / Mathews, F.S.
#1: Journal: Structure / Year: 1998
Title: Copper Amine Oxidase from Hansenula polymorpha: the Crystal Structure Determined at 2.4 A Resolution Reveals the Active Conformation
Authors: Li, R. / Klinman, J.P. / Mathews, F.S.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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_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_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

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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)221,3906
Polymers221,1933
Non-polymers1963
Water26,5901476
1
A: COPPER AMINE OXIDASE
B: COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,5934
Polymers147,4622
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-65 kcal/mol
Surface area43850 Å2
MethodPISA
2
C: COPPER AMINE OXIDASE
hetero molecules

C: COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,5934
Polymers147,4622
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
3
A: COPPER AMINE OXIDASE
B: COPPER AMINE OXIDASE
C: COPPER AMINE OXIDASE
hetero molecules

A: COPPER AMINE OXIDASE
B: COPPER AMINE OXIDASE
C: COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,77912
Polymers442,3876
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area48080 Å2
ΔGint-231 kcal/mol
Surface area125530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.227, 153.515, 223.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.91741, 0.19856, -0.34488), (0.20499, -0.50703, -0.8372), (-0.3411, -0.83875, 0.42445)12.02865, 102.3173, 63.04497
2given(0.91445, 0.21252, 0.34442), (-0.20363, -0.49386, 0.84537), (0.34975, -0.84317, -0.40833)-27.07656, 7.40864, 109.86537
DetailsMolecule is homodimer in solution. The biological unit is a dimer. Three dimers form a crystallographic hexamer which is non-biological. The asymmetric unit contains half of a hexamer, chains ABC. Chains B,C were not treated as independent during refinement but were generated by strict non-crystallographic symmetry.

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Components

#1: Protein COPPER AMINE OXIDASE


Mass: 73731.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: ZINC-SUBSTITUTED / Source: (gene. exp.) Pichia angusta (fungus) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P12807, EC: 1.4.3.6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1476 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
29-14 %PEG80001drop
3100-300 mMpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→500 Å / Num. all: 65122 / Num. obs: 64796 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.185 / Num. unique all: 3689 / % possible all: 40.7
Reflection
*PLUS
% possible obs: 77.4 % / Num. measured all: 226364
Reflection shell
*PLUS
% possible obs: 40.7 % / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.5→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED STRICT NCS CONSTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6524 -RANDOM
Rwork0.183 ---
obs0.183 64455 77.9 %-
all-64796 --
Refinement stepCycle: LAST / Resolution: 2.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 1 492 5690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.69
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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