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- PDB-1vlx: STRUCTURE OF ELECTRON TRANSFER (COBALT-PROTEIN) -

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Basic information

Entry
Database: PDB / ID: 1vlx
TitleSTRUCTURE OF ELECTRON TRANSFER (COBALT-PROTEIN)
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / COPPER / PERIPLASMIC
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 1.9 Å
AuthorsBonander, N. / Vanngard, T. / Tsai, L.-C. / Langer, V. / Nar, H. / Sjolin, L.
Citation
Journal: Proteins / Year: 1997
Title: The metal site of Pseudomonas aeruginosa azurin, revealed by a crystal structure determination of the Co(II) derivative and Co-EPR spectroscopy.
Authors: Bonander, N. / Vanngard, T. / Tsai, L.C. / Langer, V. / Nar, H. / Sjolin, L.
#1: Journal: To be Published
Title: X-Ray Structure Determination and Characterization of the Pseudomonas Aeruginosa Azurin Mutant met121Glu
Authors: Karlsson, B.G. / Tsai, L.-C. / Nar, H. / Sanders-Loehr, J. / Bonander, N. / Langer, V. / Sjoelin, L.
History
DepositionOct 8, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_asym_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
C: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0838
Polymers55,8474
Non-polymers2364
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.400, 80.400, 110.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AZURIN / COBALT-AXURIN


Mass: 13961.799 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: COBALT FORM / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: P00282
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.7
Details: THE BLUISH WELL-FORMED PRISMATIC CRYSTALS OF THE TITLE PROTEIN WERE OBTAINED BY THE VAPOR-DIFFUSION HANGING-DROP TECHNIQUE FROM A SOLUTION CONTAINING 3.6M AMMONIUM SULFATE, 0.5M LITHIUM ...Details: THE BLUISH WELL-FORMED PRISMATIC CRYSTALS OF THE TITLE PROTEIN WERE OBTAINED BY THE VAPOR-DIFFUSION HANGING-DROP TECHNIQUE FROM A SOLUTION CONTAINING 3.6M AMMONIUM SULFATE, 0.5M LITHIUM NITRATE AND 0.1M ACETATE BUFFER AT PH 5.7 AND AT THE TEMPERATURE OF 24 - 25 CENTIGRADE IN AROUND 10 DAYS., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 24-25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.6 Mammonium sulfate1reservoir
20.5 Mlithium nitrate1reservoir
30.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 0.7107
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 17, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. obs: 31366 / % possible obs: 79.7 % / Observed criterion σ(I): 2 / Redundancy: 1.84 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085
Reflection shellResolution: 1.899→1.967 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.72 / Rsym value: 0.448
Reflection
*PLUS
Num. measured all: 52176

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Processing

Software
NameClassification
SAINTdata scaling
X-PLORrefinement
X-PLORmodel building
SAINTdata reduction
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: WILD-TYPE AZURIN

Rfactor Rwork: 0.175 / Rfactor obs: 0.175 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 4 373 4273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.88
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
Num. reflection obs: 30862
Solvent computation
*PLUS
Displacement parameters
*PLUS

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