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- PDB-1e5z: Azurin from Pseudomonas aeruginosa, reduced form, pH 9.0 -

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Basic information

Entry
Database: PDB / ID: 1e5z
TitleAzurin from Pseudomonas aeruginosa, reduced form, pH 9.0
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / COPPER BINDING
Function / homology
Function and homology information


transition metal ion binding / electron transfer activity / periplasmic space / 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
COPPER (II) ION / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsNar, H. / Messerschmidt, A.
Citation
Journal: Ph.D. Thesis / Year: 1992
Title: Rontgenkristallographische Strukturaufklarung Von Azurin Aus Pseudomonas Aeruginosa
Authors: Nar, H.
#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 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,1639
Polymers55,8474
Non-polymers3165
Water5,080282
1
B: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0514
Polymers27,9242
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-11.6 kcal/mol
Surface area12080 Å2
MethodPISA
2
A: AZURIN
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1135
Polymers27,9242
Non-polymers1893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-11.5 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 81.020, 109.990
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: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growpH: 9 / Details: PH 9.0

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 22, 1991
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34847 / % possible obs: 90 % / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.075 / Rsym value: 0.07
Reflection shellResolution: 2→2.05 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
X-PLOR2.1refinement
MOSFLMdata reduction
ABSCALEdata scaling
Agrovatadata scaling
X-PLOR2.1phasing
RefinementMethod to determine structure: OTHER / Resolution: 2→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 31599 90 %
Displacement parametersBiso mean: 18.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 8 282 4186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.9
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: 2→2.1 Å / Rfactor Rwork: 0.273
Xplor fileSerial no: 1 / Param file: PARA19X.PRO / Topol file: TOPH19X.PRO

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