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- PDB-1aso: X-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL... -

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Entry
Database: PDB / ID: 1aso
TitleX-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL DERIVATIVES OF ASCORBATE OXIDASE FROM ZUCCHINI: REDUCED-, PEROXIDE-, AND AZIDE-FORMS
ComponentsASCORBATE OXIDASEL-ascorbate oxidase
KeywordsOXIDOREDUCTASE
Function / homologyMulticopper oxidases, conserved site / Multicopper oxidase / Multicopper oxidases signature 2. / Multicopper oxidases signature 1. / Multicopper oxidase, type 1 / Multicopper oxidase, copper-binding site / Cupredoxin / Multicopper oxidase, type 2 / Multicopper oxidase, type 3 / L-ascorbate oxidase, plants ...Multicopper oxidases, conserved site / Multicopper oxidase / Multicopper oxidases signature 2. / Multicopper oxidases signature 1. / Multicopper oxidase, type 1 / Multicopper oxidase, copper-binding site / Cupredoxin / Multicopper oxidase, type 2 / Multicopper oxidase, type 3 / L-ascorbate oxidase, plants / Multicopper oxidase / Ascorbate oxidase, second cupredoxin domain / Ascorbate oxidase, first cupredoxin domain / Ascorbate oxidase, third cupredoxin domain / Multicopper oxidase / L-ascorbate oxidase / L-ascorbate oxidase activity / copper ion binding / extracellular region / L-ascorbate oxidase
Function and homology information
Specimen sourceCucurbita pepo var. melopepo (zucchini)
MethodX-RAY DIFFRACTION / 2.2 Å resolution
AuthorsMesserschmidt, A. / Luecke, H. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini. Reduced, peroxide and azide forms.
Authors: Messerschmidt, A. / Luecke, H. / Huber, R.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Crystal Structure of Ascorbate Oxidase at 1.9 Angstroms Resolution
Authors: Messerschmidt, A. / Ladenstein, R. / Huber, R. / Bolognesi, M. / Avigliano, L. / Petruzzelli, R. / Rossi, A. / Finazzi-Agro, A.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: X-Ray Crystal Structure of the Blue Oxidase Ascorbate Oxidase from Zucchini. Analysis of the Polypeptide Fold and Model of the Copper Sites and Ligands
Authors: Messerschmidt, A. / Rossi, A. / Ladenstein, R. / Huber, R. / Bolognesi, M. / Gatti, G. / Marchesini, A. / Petruzzelli, R. / Finazzi-Agro, A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 25, 1992 / Release: Jan 31, 1994
RevisionDateData content typeGroupProviderType
1.0Jan 31, 1994Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASCORBATE OXIDASE
B: ASCORBATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,58515
Polyers123,5372
Non-polymers1,04813
Water17,457969
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3120
ΔGint (kcal/M)-99
Surface area (Å2)43540
MethodPISA
2
A: ASCORBATE OXIDASE
B: ASCORBATE OXIDASE
hetero molecules

A: ASCORBATE OXIDASE
B: ASCORBATE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,17130
Polyers247,0744
Non-polymers2,09726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area (Å2)13970
ΔGint (kcal/M)-229
Surface area (Å2)79350
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)106.090, 105.210, 112.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
Atom site foot note1: CIS PROLINE - PRO A 32 / 2: CIS PROLINE - PRO A 160 / 3: CIS PROLINE - PRO A 300
4: ASN A 551 - PRO A 552 OMEGA = 89.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO B 32 / 6: CIS PROLINE - PRO B 160 / 7: CIS PROLINE - PRO B 300
8: ASN B 551 - PRO B 552 OMEGA = 75.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein/peptide ASCORBATE OXIDASE / L-ascorbate oxidase


Mass: 61768.562 Da / Num. of mol.: 2
Source: (gene. exp.) Cucurbita pepo var. melopepo (zucchini)
Genus: Cucurbita / Species: Cucurbita pepo / Strain: var. melopepo / References: UniProt: P37064, L-ascorbate oxidase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Formula: Cu / Copper
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Formula: HO / Hydroxide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 / Density percent sol: 51.63 %
Crystal grow
*PLUS
pH: 5.5 / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
115 mg/mlprotein1drop
250 mMsodium phosphate1drop
350 mMsodium phosphate1reservoir
420 %(v/v)MPD1reservoir
54 %(v/v)ethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.2 Å / Number obs: 62597 / Number measured all: 323865 / Rmerge I obs: 0.213
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.32 Å / Rmerge I obs: 0.901

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.196 / R factor obs: 0.196 / Highest resolution: 2.2 Å
Refine hist #LASTHighest resolution: 2.2 Å
Number of atoms included #LASTProtein: 8732 / Nucleic acid: 0 / Ligand: 39 / Solvent: 969 / Total: 9740
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.196 / R factor obs: 0.196 / Highest resolution: 2.2 Å / Lowest resolution: 8 Å
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.99

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