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- PDB-1ui7: Site-directed mutagenesis of His433 involved in binding of copper... -

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Basic information

Entry
Database: PDB / ID: 1ui7
TitleSite-directed mutagenesis of His433 involved in binding of copper ion in Arthrobacter globiformis amine oxidase
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / copper / amine oxidase / quinone cofactor / TPQ / histidine / metal coordination
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like 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 ...: / AGAO-like 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 / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMatsunami, H. / Okajima, T. / Hirota, S. / Yamaguchi, H. / Hori, H. / Kuroda, S. / Tanizawa, K.
CitationJournal: Biochemistry / Year: 2004
Title: Chemical rescue of a site-specific mutant of bacterial copper amine oxidase for generation of the topa quinone cofactor
Authors: Matsunami, H. / Okajima, T. / Hirota, S. / Yamaguchi, H. / Hori, H. / Kuroda, S. / Tanizawa, K.
History
DepositionJul 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylethylamine oxidase
B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,5666
Polymers141,3112
Non-polymers2544
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-61 kcal/mol
Surface area40790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.510, 63.320, 185.212
Angle α, β, γ (deg.)90.00, 111.50, 90.00
Int Tables number5
Space group name H-MI121
DetailsThe biological assembly is a dimer corresponding to the asymmetric unit: x, y, z.

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Components

#1: Protein Phenylethylamine oxidase / Copper Amine oxidase


Mass: 70655.688 Da / Num. of mol.: 2 / Mutation: H433A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pEPO-02 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, EC: 1.4.3.6
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.91 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 6.8
Details: potassium sodium tartrate, pH 6.8, MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 18, 1999
RadiationMonochromator: fix-exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.06 Å / Num. all: 107342 / Num. obs: 107167 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2→2.07 Å / % possible all: 71.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 3782 RANDOM
Rwork0.206 --
all0.251 106041 -
obs0.21 75531 -
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9722 0 4 759 10485

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