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- PDB-3uge: Silver Metallated Pseudomonas aeruginosa Azurin at 1.70 A -

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Basic information

Entry
Database: PDB / ID: 3uge
TitleSilver Metallated Pseudomonas aeruginosa Azurin at 1.70 A
ComponentsAzurin
KeywordsELECTRON 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 / 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPanzner, M.J. / Billinovich, S.M. / Parker, J.A. / Bladholm, E. / Berry, S.M. / Ziegler, C.J. / Leeper, T.C.
CitationJournal: To be Published
Title: Silver Metallation of Pseudomonas aeruginosa Azurin
Authors: Panzner, M.J. / Billinovich, S.M. / Parker, J.A. / Bladholm, E. / Berry, S.M. / Ziegler, C.J. / Leeper, T.C.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source / _diffrn_source.type
Revision 1.2Sep 13, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 1.3Oct 30, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2798
Polymers55,8474
Non-polymers4314
Water6,287349
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0702
Polymers13,9621
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0702
Polymers13,9621
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0702
Polymers13,9621
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0702
Polymers13,9621
Non-polymers1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.746, 97.815, 110.029
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: 13961.799 Da / Num. of mol.: 4 / Fragment: UNP residues 21-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 1 mM silver nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→36.68 Å / Num. all: 64687 / Num. obs: 64144 / % possible obs: 99.2 % / Redundancy: 7.35 % / Rsym value: 0.109 / Net I/σ(I): 10.97
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.33 % / Mean I/σ(I) obs: 2.04 / % possible all: 100

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Processing

Software
NameVersionClassification
APEXdata collection
REFMAC5.2.0019refinement
SAINTdata reduction
APEXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E67

1e67


Resolution: 1.7→29.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.459 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.117 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24459 2965 5.1 %RANDOM
Rwork0.2035 ---
obs0.20556 55707 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 4 349 4249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223977
X-RAY DIFFRACTIONr_bond_other_d0.0010.022616
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9515370
X-RAY DIFFRACTIONr_angle_other_deg0.8943.0026463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53626.45169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15615709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.826154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_nbd_refined0.2090.2755
X-RAY DIFFRACTIONr_nbd_other0.1930.22687
X-RAY DIFFRACTIONr_nbtor_refined0.170.21942
X-RAY DIFFRACTIONr_nbtor_other0.0860.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.340.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0991.53290
X-RAY DIFFRACTIONr_mcbond_other0.2261.51050
X-RAY DIFFRACTIONr_mcangle_it1.27224087
X-RAY DIFFRACTIONr_scbond_it2.10531645
X-RAY DIFFRACTIONr_scangle_it3.0264.51283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free3.08434
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 228 -
Rwork0.236 4079 -
obs--100 %

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