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- PDB-1etj: AZURIN MUTANT WITH MET 121 REPLACED BY GLU -

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Basic information

Entry
Database: PDB / ID: 1etj
TitleAZURIN MUTANT WITH MET 121 REPLACED BY GLU
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 / 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
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarlsson, B.G. / Tsai, L.-C. / Nar, H. / Sanders-Loehr, J. / Bonander, N. / Langer, V. / Sjolin, L.
CitationJournal: Biochemistry / Year: 1997
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. / Sjolin, L.
History
DepositionJan 11, 1997Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,0938
Polymers55,8394
Non-polymers2544
Water5,549308
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0232
Polymers13,9601
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0232
Polymers13,9601
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0232
Polymers13,9601
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0232
Polymers13,9601
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.580, 60.940, 81.600
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AZURIN


Mass: 13959.717 Da / Num. of mol.: 4 / Mutation: M121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / References: UniProt: P00282
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.25 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: THE BLUISH WELL-FORMED PRISMATIC CRYSTALS OF THE TITLE PROTEIN WERE OBTAINED BY THE VAPOR-DIFFUSION HANGING-DROP TECHNIQUE FROM A SOLUTION CONTAINING 25% PEG4000, 0.24M CALCIUM DICHLORIDE ...Details: THE BLUISH WELL-FORMED PRISMATIC CRYSTALS OF THE TITLE PROTEIN WERE OBTAINED BY THE VAPOR-DIFFUSION HANGING-DROP TECHNIQUE FROM A SOLUTION CONTAINING 25% PEG4000, 0.24M CALCIUM DICHLORIDE AND 0.26M LITHIUM NITRATE BUFFER AT PH 6.0 AND AT THE TEMPERATURE OF 24 - 25 CENTIGRADE IN AROUND 10 DAYS., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 g/Lprotein11
225 %PEG400012
380 mMsodium acetate12
480 mM12CaCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→8 Å / Num. obs: 17964 / % possible obs: 75.7 % / Observed criterion σ(I): 2 / Redundancy: 2.77 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115
Reflection
*PLUS
Num. measured all: 47678

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Processing

Software
NameClassification
MADNESdata collection
X-PLORrefinement
X-PLORmodel building
MADNESdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE AZURIN MONOMER

Rfactor Rwork: 0.184 / Rfactor obs: 0.184 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 4 308 4212
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_deg3.18
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
Lowest resolution: 8 Å / Num. reflection obs: 15836
Solvent computation
*PLUS
Displacement parameters
*PLUS

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