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- PDB-1aoz: REFINED CRYSTAL STRUCTURE OF ASCORBATE OXIDASE AT 1.9 ANGSTROMS R... -

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Basic information

Entry
Database: PDB / ID: 1aoz
TitleREFINED CRYSTAL STRUCTURE OF ASCORBATE OXIDASE AT 1.9 ANGSTROMS RESOLUTION
ComponentsASCORBATE OXIDASE
KeywordsOXIDOREDUCTASE(OXYGEN ACCEPTOR)
Function / homology
Function and homology information


L-ascorbate oxidase / L-ascorbate oxidase activity / plasmodesma / copper ion binding / extracellular region
Similarity search - Function
L-ascorbate oxidase, plants / Ascorbate oxidase, second cupredoxin domain / Ascorbate oxidase, first cupredoxin domain / Ascorbate oxidase, third cupredoxin domain / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase ...L-ascorbate oxidase, plants / Ascorbate oxidase, second cupredoxin domain / Ascorbate oxidase, first cupredoxin domain / Ascorbate oxidase, third cupredoxin domain / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CU-O LINKAGE / CU-O-CU LINKAGE / COPPER (II) ION / L-ascorbate oxidase
Similarity search - Component
Biological speciesCucurbita pepo var. melopepo (plant)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMesserschmidt, A. / Ladenstein, R. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined crystal structure of ascorbate oxidase at 1.9 A resolution.
Authors: Messerschmidt, A. / Ladenstein, R. / Huber, R. / Bolognesi, M. / Avigliano, L. / Petruzzelli, R. / Rossi, A. / Finazzi-Agro, A.
#1: 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 a 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.
History
DepositionJan 8, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)124,61511
Polymers123,5372
Non-polymers1,0789
Water17,475970
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-74 kcal/mol
Surface area43620 Å2
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)249,23122
Polymers247,0744
Non-polymers2,15718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13110 Å2
ΔGint-176 kcal/mol
Surface area79880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 105.100, 113.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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 ANGLE = 88.478 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 ANGLE = 76.915 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-1029-

HOH

21B-946-

HOH

31B-1034-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ASCORBATE OXIDASE


Mass: 61768.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucurbita pepo var. melopepo (plant) / Species: Cucurbita pepo / Strain: var. melopepo / References: UniProt: P37064, L-ascorbate oxidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 977 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O
#5: Chemical ChemComp-C1O / CU-O LINKAGE


Mass: 79.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CuO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Details: referred to 'Bolognesi, M.', (1983) J. Mol. Biol., 169, 351-352
PH range low: 5.8 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein11
210 %(v/v)MPD12
30.05 Mphosphate1

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 86529 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Num. measured all: 249029 / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8732 0 41 970 9743
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 85252 / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.8 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.99

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