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

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Basic information

Entry
Database: PDB / ID: 1ilu
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 / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / software / 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_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 / _software.name / _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 1.4Oct 9, 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
E: AZURIN
F: AZURIN
G: AZURIN
H: AZURIN
I: AZURIN
K: AZURIN
L: AZURIN
M: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,58324
Polymers166,82012
Non-polymers76312
Water12,899716
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
K: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
L: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
M: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9652
Polymers13,9021
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.400, 170.100, 99.700
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AZURIN


Mass: 13901.702 Da / Num. of mol.: 12 / Mutation: F110S
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.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
20.1 Msodium acetate1drop
32.5 Mammonium sulfate1drop
40.6 Mlithium nitrate1drop
53.5 Mammonium sulfate1reservoir
61.0 Mlithium nitrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 54140 / % possible obs: 86.3 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106
Reflection
*PLUS
Num. measured all: 81888 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 2.37 Å / % possible obs: 74.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4(ROTAVATAdata collection
Agrovatadata collection
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.171 -
obs0.171 51595
Displacement parametersBiso mean: 23.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14268 0 12 2148 16428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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