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

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Entry
Database: PDB / ID: 1asq
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 / homology
Function and homology information


L-ascorbate oxidase / L-ascorbate oxidase activity / 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 oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase / Multicopper oxidase, C-terminal ...L-ascorbate oxidase, plants / Ascorbate oxidase, second cupredoxin domain / Ascorbate oxidase, first cupredoxin domain / Ascorbate oxidase, third cupredoxin domain / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AZIDE ION / COPPER (II) ION / HYDROXIDE ION / L-ascorbate oxidase
Similarity search - Component
Biological speciesCucurbita pepo (plant)
MethodX-RAY DIFFRACTION / Resolution: 2.32 Å
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.
History
DepositionNov 25, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 / pdbx_struct_special_symmetry / 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_asym_id / _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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,75419
Polymers123,5372
Non-polymers1,21617
Water17,475970
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-101 kcal/mol
Surface area43480 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)249,50738
Polymers247,0744
Non-polymers2,43334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15200 Å2
ΔGint-232 kcal/mol
Surface area79400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.320, 105.280, 113.000
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 = 82.66 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 = 78.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-778-

HOH

21B-796-

HOH

31B-882-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ASCORBATE OXIDASE / L-ascorbate oxidase


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


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, 985 molecules

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


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water / Water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal grow
*PLUS
pH: 5.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common 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
Highest resolution: 2.32 Å / Num. obs: 52722 / Num. measured all: 211636 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.32 Å / Lowest resolution: 2.46 Å / Rmerge(I) obs: 0.51

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.178 / Rfactor obs: 0.178 / Highest resolution: 2.32 Å
Refinement stepCycle: LAST / Highest resolution: 2.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8732 0 51 970 9753
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
Refinement
*PLUS
Highest resolution: 2.32 Å / Lowest resolution: 8 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.99

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