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- PDB-1oac: CRYSTAL STRUCTURE OF A QUINOENZYME: COPPER AMINE OXIDASE OF ESCHE... -

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Basic information

Entry
Database: PDB / ID: 1oac
TitleCRYSTAL STRUCTURE OF A QUINOENZYME: COPPER AMINE OXIDASE OF ESCHERICHIA COLI AT 2 ANGSTROEMS RESOLUTION
ComponentsCOPPER AMINE OXIDASE
KeywordsOXIDOREDUCTASE / COPPER / TPQ / PERIPLASMIC
Function / homology
Function and homology information


phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding
Similarity search - Function
Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / 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-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Primary amine oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsParsons, M.R. / Convery, M.A. / Wilmot, C.M. / Phillips, S.E.V.
CitationJournal: Structure / Year: 1995
Title: Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution.
Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F.
History
DepositionSep 27, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0218
Polymers162,7332
Non-polymers2876
Water17,439968
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-94 kcal/mol
Surface area50530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.732, 167.775, 81.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 697 / 2: CIS PROLINE - PRO B 697
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.35014, -0.93668, -0.00524), (-0.93669, -0.35015, 0.00116), (-0.00292, 0.0045, -0.99999)
Vector: 90.40221, 130.35484, 8.27297)
DetailsE. COLI AMINE OXIDASE IS A HOMODIMER. EACH SUBUNIT CONTAIN ONE COPPER AND A REDOX COFACTOR, TPQ, IN THE ACTIVE SITE. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 727 B 5 .. B 727 0.570

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Components

#1: Protein COPPER AMINE OXIDASE


Mass: 81366.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P46883, EC: 1.4.3.6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / 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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.3 Mammonium sulfate1reservoir
2100 mMHEPES1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.891
ReflectionResolution: 2→20 Å / Num. obs: 435398 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
MOSFLMdata reduction
PROLSQrefinement
RefinementResolution: 2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.162 109741
Displacement parametersBiso mean: 29.34 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11384 0 6 968 12358
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0410.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0610.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8184
X-RAY DIFFRACTIONp_mcangle_it4.015
X-RAY DIFFRACTIONp_scbond_it4.8965
X-RAY DIFFRACTIONp_scangle_it7.2756
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1120.12
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2530.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.170.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor9.83720
X-RAY DIFFRACTIONp_staggered_tor18.51530
X-RAY DIFFRACTIONp_orthonormal_tor23.1250
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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