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- PDB-2gi0: Crystal structure of Cu(I) Phe114Pro Azurin mutant -

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Basic information

Entry
Database: PDB / ID: 2gi0
TitleCrystal structure of Cu(I) Phe114Pro Azurin mutant
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Azurin / blue copper protein / metal binding site
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein 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 (I) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Direct use of Cu(II) structure in refinement / Resolution: 1.7 Å
AuthorsYanagisawa, S. / Banfield, M.J. / Dennison, C.
CitationJournal: Biochemistry / Year: 2006
Title: The role of hydrogen bonding at the active site of a cupredoxin: the Phe114Pro azurin variant.
Authors: Yanagisawa, S. / Banfield, M.J. / Dennison, C.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 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 1.5Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9514
Polymers27,8232
Non-polymers1272
Water5,711317
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9752
Polymers13,9121
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9752
Polymers13,9121
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.39, 47.86, 132.55
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsProtein is a monomer in solution

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Components

#1: Protein Azurin


Mass: 13911.739 Da / Num. of mol.: 2 / Mutation: Phe114Pro
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00282
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% PEG1500, 100mM MMT buffer, pH4. To generate Cu(I), Cu(II) containing crystals were reduced by soaking in reservoir solution with 10mM ascorbate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2005 / Details: Osmic 'blue'
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.551→66.275 Å / Num. all: 24113 / Num. obs: 24113 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 6
Reflection shellResolution: 1.7→1.79 Å / % possible obs: 85.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Num. measured all: 16231 / Num. unique all: 3111 / Num. unique obs: 3111 / Rsym value: 0.287 / % possible all: 85.6

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Direct use of Cu(II) structure in refinement
Starting model: 2GHZ

2ghz


Resolution: 1.7→47.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.299 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1208 5 %RANDOM
Rwork0.179 ---
all0.181 24057 --
obs0.181 24057 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 2 317 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222017
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9562746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9975276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65526.58582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.621152
X-RAY DIFFRACTIONr_chiral_restr0.110.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021512
X-RAY DIFFRACTIONr_nbd_refined0.210.21103
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2261
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.229
X-RAY DIFFRACTIONr_mcbond_it1.0791.51344
X-RAY DIFFRACTIONr_mcangle_it1.57322109
X-RAY DIFFRACTIONr_scbond_it2.5053761
X-RAY DIFFRACTIONr_scangle_it3.7594.5626
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 74 -
Rwork0.295 1484 -
obs-1558 85.14 %

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