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- PDB-1dyz: OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS -

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Basic information

Entry
Database: PDB / ID: 1dyz
TitleOXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS
ComponentsAZURIN II
KeywordsELECTRON TRANSPORT / CUPREDOXIN / CUPROPROTEIN
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / : / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Azurin-2
Similarity search - Component
Biological speciesALCALIGENES XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDodd, F.E. / Abraham, Z.H.L. / Eady, R.R. / Hasnain, S.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structures of Oxidised and Reduced Azurin II from Alcaligenes Xylosoxidans at 1.75 Angstoms Resolution
Authors: Dodd, F.E. / Abraham, Z.H.L. / Eady, R.R. / Hasnain, S.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of a New Azurin from Alcaligenes Xylosoxidans at High Resolution
Authors: Dodd, F.E. / Hasnain, S.S. / Abraham, Z.H.L. / Eady, R.R. / Smith, B.E.
History
DepositionFeb 11, 2000Deposition site: PDBE / Processing site: PDBE
SupersessionJul 10, 2000ID: 1ARN
Revision 1.0Jul 10, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8572
Polymers13,7941
Non-polymers641
Water1,18966
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.650, 52.650, 100.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein AZURIN II


Mass: 13793.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCIMB 11015 / Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P56275
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 52 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 6
Details: 0.1M KH2 PO4 PH 6.0, 60% SATURATED AMMONIUM SULPHATE
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 M1dropKH2PO4
40.1 M1reservoirKH2PO4
3ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI BAS-2000 IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.2 Å / Num. obs: 12084 / % possible obs: 82.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.1 / % possible all: 53.6
Reflection
*PLUS
Num. measured all: 34438
Reflection shell
*PLUS
% possible obs: 53.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
WEISdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ARN

1arn
PDB Unreleased entry


Resolution: 1.75→8.5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DPI = 0.09 ANGSTOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1060 10 %RANDOM
Rwork0.189 ---
obs0.189 10290 82.2 %-
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 1 66 1024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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