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

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Basic information

Entry
Database: PDB / ID: 3fsw
TitlePseudomonas aeruginosa Azurin with mutated metal-binding loop sequence (CAAAAHAAAM)
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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
B: Azurin
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3978
Polymers55,1424
Non-polymers2544
Water4,197233
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8492
Polymers13,7861
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.686, 56.700, 58.242
Angle α, β, γ (deg.)111.96, 95.38, 105.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Azurin


Mass: 13785.584 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMETAL BINDING LOOP MUTATED TO CAAAAHAAAM

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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: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Hepes pH 8.0, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→49.8 Å / Num. all: 25606 / Num. obs: 25606 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3332 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FS9

3fs9


Resolution: 2→49.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.619 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25573 1309 5.1 %RANDOM
Rwork0.18922 ---
all0.19267 24283 --
obs0.19267 24283 92.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.5 Å20.24 Å2
2--0.25 Å20.12 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 4 233 3981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213850
X-RAY DIFFRACTIONr_bond_other_d0.0010.022428
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9395227
X-RAY DIFFRACTIONr_angle_other_deg0.8283.0036009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18226.564163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59515639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.877154
X-RAY DIFFRACTIONr_chiral_restr0.0680.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
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_it0.4691.52522
X-RAY DIFFRACTIONr_mcbond_other0.0841.51043
X-RAY DIFFRACTIONr_mcangle_it0.84524040
X-RAY DIFFRACTIONr_scbond_it1.26331328
X-RAY DIFFRACTIONr_scangle_it2.0024.51180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 81 -
Rwork0.241 1678 -
obs--86.35 %

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