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- PDB-1uri: AZURIN MUTANT WITH MET 121 REPLACED BY GLN -

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Basic information

Entry
Database: PDB / ID: 1uri
TitleAZURIN MUTANT WITH MET 121 REPLACED BY GLN
ComponentsAZURIN
KeywordsELECTRON TRANSPORT / COPPER / PERIPLASMIC
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion 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 / Azurin
Similarity search - Component
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsRomero, A. / Nar, H. / Huber, R. / Messerschmidt, A.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: X-ray analysis and spectroscopic characterization of M121Q azurin. A copper site model for stellacyanin.
Authors: Romero, A. / Hoitink, C.W. / Nar, H. / Huber, R. / Messerschmidt, A. / Canters, G.W.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Azurin from Alcaligenes Denitrificans
Authors: Baker, E.N.
History
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AZURIN
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3296
Polymers28,0102
Non-polymers3194
Water3,441191
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1653
Polymers14,0051
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1653
Polymers14,0051
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.480, 74.340, 98.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein AZURIN


Mass: 14004.936 Da / Num. of mol.: 2 / Mutation: M121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans (bacteria) / Strain: JM101 / Plasmid: PCH5 / Production host: Escherichia coli (E. coli) / References: UniProt: P00280
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal grow
*PLUS
pH: 5.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
20.1 MNa, K phosphate1drop
32 Mammonium sulfate1drop
460 %(w/v)satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 2, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16824 / % possible obs: 79 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 9999 Å / Num. measured all: 58815
Reflection shell
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 1.99 Å / % possible obs: 27.2 %

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 1.94→8 Å / σ(F): 2
Details: BESIDES GLYCINE RESIDUES, ONLY WEAKLY DEFINED RESIDUES FROM THE N-TERMINAL (GLN 2) LIE OUTSIDE THE ALLOWED REGIONS IN THE RAMACHANDRAN PLOT.
RfactorNum. reflection
Rwork0.173 -
obs0.173 16171
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 1.94→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 12 191 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.834
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 1.99 Å / Rfactor all: 0.306

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