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- PDB-1ils: X-RAY CRYSTAL STRUCTURE THE TWO SITE-SPECIFIC MUTANTS ILE7SER AND... -

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Basic information

Entry
Database: PDB / ID: 1ils
TitleX-RAY CRYSTAL STRUCTURE THE TWO SITE-SPECIFIC MUTANTS ILE7SER AND PHE110SER OF AZURIN FROM PSEUDOMONAS AERUGINOSA
ComponentsAZURIN
KeywordsMETALLOPROTEIN / ELECTRON TRANSFER PROTEIN
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 / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHammann, C. / Nar, H. / Huber, R. / Messerschmidt, A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: X-ray crystal structure of the two site-specific mutants Ile7Ser and Phe110Ser of azurin from Pseudomonas aeruginosa.
Authors: Hammann, C. / Messerschmidt, A. / Huber, R. / Nar, H. / Gilardi, G. / 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
DepositionOct 12, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: 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 / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)56,0599
Polymers55,7434
Non-polymers3165
Water5,819323
1
A: AZURIN
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0615
Polymers27,8712
Non-polymers1893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-12 kcal/mol
Surface area11860 Å2
MethodPISA
2
B: AZURIN
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9994
Polymers27,8712
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-12 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 80.700, 110.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AZURIN


Mass: 13935.720 Da / Num. of mol.: 4 / Mutation: I7S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): JM101 / 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: 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.: 323 / 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: 2.29 Å3/Da / Density % sol: 46.35 %

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 18407 / % possible obs: 73.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077
Reflection
*PLUS
Num. measured all: 92017 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 21.6 %

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Processing

Software
NameVersionClassification
MADNESdata collection
ABSCORdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
ABSCORdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.169 -
obs0.169 17877
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4768 0 8 969 5745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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