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- PDB-1e67: Zn-Azurin from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1.0E+67
TitleZn-Azurin from Pseudomonas aeruginosa
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 / plasma membrane
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
NITRATE ION / Azurin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.14 Å
AuthorsNar, H. / Messerschmidt, A.
Citation
Journal: Eur.J.Biochem. / Year: 1992
Title: Characterization and Crystal Structure of Zinc Azurin, a by-Product of Heterologous Expression in Escherichia Coli of Pseudomonas Aeruginosa Copper Azurin
Authors: Nar, H. / Huber, R. / Messerschmidt, A. / Filippou, A.C. / Barth, M. / Jaquinod, M. / Van De Kamp, M.
#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 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: 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
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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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)56,1719
Polymers55,8474
Non-polymers3245
Water5,801322
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0893
Polymers13,9621
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0272
Polymers13,9621
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0272
Polymers13,9621
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0272
Polymers13,9621
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.490, 80.650, 110.150
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO3 / NITRATE ION


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


Mass: 18.015 Da / Num. of mol.: 322 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 5.7 / Details: pH 5.70
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion / Details: Nar, H., (1991) J.Mol.Biol., 221, 765.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
21.5 Mammonium sulfate1drop
30.1 Mlithium nitrate1drop
40.1 Macetate1drop
54.0 Mammonium sulfate1reservoir
60.7 Mlithium nitrate1reservoir
70.1 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: Jun 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: 2.14→50 Å / Num. obs: 26009 / % possible obs: 79.1 % / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.109 / Rsym value: 0.103
Reflection shellResolution: 2.14→2.25 Å / % possible all: 44.2
Reflection shell
*PLUS
% possible obs: 44.2 %

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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: 2.14→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 23000 69.97 %
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 8 322 4226
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: 2.14→2.2 Å / Rfactor Rwork: 0.262
Xplor fileSerial no: 1 / Param file: PARA19X.PRO / Topol file: TOPH19X.PRO

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