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- PDB-2ccw: Crystal structure of Azurin II at atomic resolution (1.13 angstrom) -

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Basic information

Entry
Database: PDB / ID: 2ccw
TitleCrystal structure of Azurin II at atomic resolution (1.13 angstrom)
ComponentsAZURIN II
KeywordsELECTRON TRANSPORT (CUPROPROTEIN) / AZURIN II / ALCALIGENES XYLOSOXIDANS / ELECTRON TRANSFER / CUPREDOXIN / ELECTRON TRANSPORT / CUPROPROTEIN / COPPER / METAL- BINDING / PERIPLASMIC
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 (I) ION / Azurin-2
Similarity search - Component
Biological speciesALCALIGENES XYLOSOXYDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsParaskevopoulos, K. / Hough, M.A. / Eady, R.R. / Hasnain, S.S.
CitationJournal: Dalton Trans. / Year: 2006
Title: Active Site Structures and the Redox Properties of Blue Copper Proteins: Atomic Resolution Structure of Azurin II and Electronic Structure Calculations of Azurin, Plastocyanin and Stellacyanin.
Authors: Paraskevopoulos, K. / Sundararajan, M. / Surendran, R. / Hough, M.A. / Eady, R.R. / Hillier, I.H. / Hasnain, S.S.
History
DepositionJan 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.754, 51.754, 99.789
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 / AZN-2


Mass: 13793.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACHROMOBACTER XYLOSOXIDANS / Source: (natural) ALCALIGENES XYLOSOXYDANS (bacteria) / References: UniProt: P56275
#2: Chemical ChemComp-CU1 / COPPER (I) 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.: 210 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAZURIN, FOUND IN BACTERIA, IS THOUGHT TO TRANSFER ELECTRONS FROM CYTOCHROME C551 TO CYTOCHROME OXIDASE.
Sequence detailsTHE CONFLICT 2CCW ALA:A:19 - UNP P56275 GLU IS ASSIGNED FROM ELECTRON DENSITY

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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: 1.93 Å3/Da / Density % sol: 35.74 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.13→51.8 Å / Num. obs: 48485 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / % possible all: 83.6

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZ0

1dz0


Resolution: 1.13→51.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor% reflectionSelection details
Rfree0.146 -RANDOM
obs0.128 94.4 %-
Refinement stepCycle: LAST / Resolution: 1.13→51.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 1 210 1168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.0001
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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