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- PDB-3fs9: Pseudomonas aeruginosa Azurin with mutated metal-binding loop seq... -

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Basic information

Entry
Database: PDB / ID: 3fs9
TitlePseudomonas aeruginosa Azurin with mutated metal-binding loop sequence (CAAHAAM)
ComponentsAzurin
KeywordsMETAL BINDING PROTEIN / cupredoxin fold / metal binding / protein-protein interaction / Electron transport / Metal-binding / Transport
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 (II) ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBanfield, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Metal-binding loop length and not sequence dictates structure.
Authors: Sato, K. / Li, C. / Salard, I. / Thompson, A.J. / Banfield, M.J. / Dennison, C.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6362
Polymers13,5721
Non-polymers641
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.774, 46.155, 58.030
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: 13572.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMETAL BINDING LOOP MUTATED TO CAAHAAM

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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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M potassium thiocyanate, 30% PEG 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.05→58 Å / Num. all: 50521 / Num. obs: 50521 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.5
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 9.1 / Num. unique all: 7235 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FT6

2ft6


Resolution: 1.05→36.13 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.592 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14528 2562 5.1 %RANDOM
Rwork0.12016 ---
all0.12145 47740 --
obs0.12145 47740 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.05→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 1 258 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221047
X-RAY DIFFRACTIONr_bond_other_d0.0010.02699
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9471440
X-RAY DIFFRACTIONr_angle_other_deg1.1173.0021739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51126.09841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43215189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.134151
X-RAY DIFFRACTIONr_chiral_restr0.4360.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021210
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02194
X-RAY DIFFRACTIONr_nbd_refined0.2390.2218
X-RAY DIFFRACTIONr_nbd_other0.1910.2754
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2507
X-RAY DIFFRACTIONr_nbtor_other0.0910.2545
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2780.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3420.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.260
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.171.5880
X-RAY DIFFRACTIONr_mcbond_other0.8141.5275
X-RAY DIFFRACTIONr_mcangle_it2.64821098
X-RAY DIFFRACTIONr_scbond_it3.1293429
X-RAY DIFFRACTIONr_scangle_it3.9434.5327
X-RAY DIFFRACTIONr_rigid_bond_restr1.54132116
X-RAY DIFFRACTIONr_sphericity_free9.7153269
X-RAY DIFFRACTIONr_sphericity_bonded4.41831711
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 192 -
Rwork0.214 3439 -
obs--98.7 %

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