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

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Basic information

Entry
Database: PDB / ID: 3fsv
TitlePseudomonas aeruginosa Azurin with mutated metal-binding loop sequence (CAAAHAAAM)
ComponentsAzurin
KeywordsMETAL BINDING PROTEIN / cupredoxin fold / metal-binding / protein-protein interaction
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 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 / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)13,7782
Polymers13,7151
Non-polymers641
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Azurin
hetero molecules

A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5564
Polymers27,4292
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4470 Å2
ΔGint-57 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.836, 55.819, 74.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-201-

CU

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Components

#1: Protein Azurin


Mass: 13714.507 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.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMETAL BINDING LOOP MUTATED TO CAAAHAAAM

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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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150mM potassium bromide, 30% PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM Q315 / Detector: CCD / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→44.7 Å / Num. all: 5240 / Num. obs: 5240 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 7.4 / Num. unique all: 755 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FS9

3fs9


Resolution: 2.3→44.68 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.757 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.551 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30839 510 9.7 %RANDOM
Rwork0.257 ---
all0.26207 4729 --
obs0.26207 4729 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.641 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---0.69 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 1 17 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021901
X-RAY DIFFRACTIONr_bond_other_d0.0010.02572
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.9281221
X-RAY DIFFRACTIONr_angle_other_deg0.7813.0031404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52926.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53515147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.386151
X-RAY DIFFRACTIONr_chiral_restr0.0650.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02164
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.5588
X-RAY DIFFRACTIONr_mcbond_other0.0541.5242
X-RAY DIFFRACTIONr_mcangle_it0.9472944
X-RAY DIFFRACTIONr_scbond_it0.8773313
X-RAY DIFFRACTIONr_scangle_it1.4014.5277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 38 -
Rwork0.307 337 -
obs--100 %

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