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- PDB-1e65: Azurin from Pseudomonas aeruginosa, apo form -

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Basic information

Entry
Database: PDB / ID: 1.0E+65
TitleAzurin from Pseudomonas aeruginosa, apo form
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / COPPER BINDING
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 / OTHER / Resolution: 1.85 Å
AuthorsNar, H. / Messerschmidt, A.
Citation
Journal: FEBS Lett. / Year: 1992
Title: Crystal Structure of Pseudomonas Aeruginosa Apo-Azurin at 1.85 A Resolution.
Authors: Nar, H. / Messerschmidt, A. / Huber, R. / Van De Kamp, M. / Canters, G.W.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystal Structure Analysis of Oxidized Pseudomonas Aeruginosa Azurin at Ph 5.5 And Ph 9.0
Authors: Nar, H. / Messerschmidt, A. / Huber, R. / Van De Kamp, M. / Canters, G.W.
History
DepositionAug 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_detector.detector / _diffrn_source.type
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name

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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


Theoretical massNumber of molelcules
Total (without water)55,8474
Polymers55,8474
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-43.4 kcal/mol
Surface area25130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.090, 81.100, 110.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1) / Vector: 20, 10, 15)

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Components

#1: Protein
AZURIN


Mass: 13961.799 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): KMBL1164 / References: UniProt: P00282
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growpH: 5.5 / Details: PH 5.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22.0 Mammonium sulfate1drop
30.3 Mlithium nirate1drop
43.2 Mammonium sulfate1reservoir
50.5 Mlithium nirate1reservoir
60.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 10, 1991
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 39493 / % possible obs: 81.1 % / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.089 / Rsym value: 0.083
Reflection shellResolution: 1.85→1.9 Å / % possible all: 20.3
Reflection
*PLUS
Num. measured all: 141499
Reflection shell
*PLUS
% possible obs: 20.3 %

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Processing

Software
NameVersionClassification
X-PLOR2.1refinement
MADNESSdata reduction
ABSCORdata scaling
PROTEINdata scaling
X-PLOR2.1phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.85→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 34350 75.9 %
Displacement parametersBiso mean: 18.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 164 4060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.94
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
LS refinement shellResolution: 1.85→1.9 Å / Rfactor Rwork: 0.356
Xplor fileSerial no: 1 / Param file: PARA19X.PRO / Topol file: TOPH19X.PRO

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