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- PDB-4hz1: Crystal Structure of Pseudomonas aeruginosa azurin with iron(II) ... -

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Basic information

Entry
Database: PDB / ID: 4hz1
TitleCrystal Structure of Pseudomonas aeruginosa azurin with iron(II) at the copper-binding site.
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Copper binding site / reductase / arsenite
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
ACETATE ION / : / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcLaughlin, M.P. / Retegan, M. / Bill, E. / Payne, T.M. / Shafaat, H.S. / Pea, S. / Sudhamsu, J. / Ensign, A.A. / Crane, B.R. / Neese, F. / Holland, P.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Azurin as a Protein Scaffold for a Low-coordinate Nonheme Iron Site with a Small-molecule Binding Pocket.
Authors: McLaughlin, M.P. / Retegan, M. / Bill, E. / Payne, T.M. / Shafaat, H.S. / Pena, S. / Sudhamsu, J. / Ensign, A.A. / Crane, B.R. / Neese, F. / Holland, P.L.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 20, 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 1.3Oct 16, 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
C: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25411
Polymers55,8474
Non-polymers4077
Water2,648147
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1394
Polymers13,9621
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0773
Polymers13,9621
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0773
Polymers13,9621
Non-polymers1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin


Theoretical massNumber of molelcules
Total (without water)13,9621
Polymers13,9621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.309, 98.033, 108.900
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00282
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 3.0 - 3.5 M ammonium sulfate, 0.5 M lithium nitrate, 0.1 M sodium acetate pH 5.2-5.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
PH range: 5.2-5.4

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.608 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.608 Å / Relative weight: 1
ReflectionResolution: 2.2→43 Å / Num. all: 26498 / Num. obs: 26498 / % possible obs: 95 % / Observed criterion σ(F): 10000 / Observed criterion σ(I): 10000 / Rsym value: 0.127 / Net I/σ(I): 13.48

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AZU

1azu


Resolution: 2.2→43 Å / σ(F): 10000 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 2643 Random
Rwork0.245 --
all-26498 -
obs-26498 -
Refinement stepCycle: LAST / Resolution: 2.2→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 22 147 4044

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