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- PDB-4jkn: Mercury Metallated Pseudomonas aeruginosa Azurin at 1.54 A -

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Basic information

Entry
Database: PDB / ID: 4jkn
TitleMercury Metallated Pseudomonas aeruginosa Azurin at 1.54 A
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Mercury metallation
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
: / NITRATE ION / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.536 Å
AuthorsZampino, A.P. / Masters, F.M. / Bladholm, E.L. / Berry, S.B. / Panzner, M.J. / Ziegler, C.J.
CitationJournal: J.Inorg.Biochem. / Year: 2014
Title: Mercury metallation of the copper protein azurin and structural insight into possible heavy metal reactivity.
Authors: Zampino, A.P. / Masters, F.M. / Bladholm, E.L. / Panzner, M.J. / Berry, S.M. / Leeper, T.C. / Ziegler, C.J.
History
DepositionMar 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 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_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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)57,38017
Polymers55,8474
Non-polymers1,53313
Water8,071448
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4875
Polymers13,9621
Non-polymers5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2243
Polymers13,9621
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1622
Polymers13,9621
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5067
Polymers13,9621
Non-polymers5456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.483, 79.228, 109.576
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) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, azu PA4922, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282, arsenate reductase (azurin)
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 3 fold excess Mercury Chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.536→28.24 Å / Num. obs: 73480 / % possible obs: 98 % / Observed criterion σ(I): 4.5
Reflection shellResolution: 1.536→1.74 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
APEXdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
SAINTdata reduction
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+67 / Resolution: 1.536→19.66 Å / SU ML: 0.21 / σ(F): 0.45 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 3682 5.04 %
Rwork0.211 --
obs0.213 73033 98.7 %
all-73049 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.536→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 38 448 4382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134086
X-RAY DIFFRACTIONf_angle_d1.4655510
X-RAY DIFFRACTIONf_dihedral_angle_d14.0721497
X-RAY DIFFRACTIONf_chiral_restr0.088614
X-RAY DIFFRACTIONf_plane_restr0.009726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5361-1.55630.38421190.36552084X-RAY DIFFRACTION78
1.5563-1.57760.35291570.33882634X-RAY DIFFRACTION100
1.5776-1.60010.31081320.32422660X-RAY DIFFRACTION100
1.6001-1.6240.30361240.30462694X-RAY DIFFRACTION100
1.624-1.64940.32251270.30322691X-RAY DIFFRACTION100
1.6494-1.67640.2981170.28672682X-RAY DIFFRACTION100
1.6764-1.70530.30621580.27042664X-RAY DIFFRACTION100
1.7053-1.73630.28291390.25722646X-RAY DIFFRACTION100
1.7363-1.76960.29261540.25042686X-RAY DIFFRACTION100
1.7696-1.80570.2831610.23992627X-RAY DIFFRACTION100
1.8057-1.8450.25041260.23232681X-RAY DIFFRACTION100
1.845-1.88790.28731310.23372696X-RAY DIFFRACTION100
1.8879-1.9350.26181470.24172642X-RAY DIFFRACTION99
1.935-1.98730.26441570.21892665X-RAY DIFFRACTION100
1.9873-2.04570.23461330.21292664X-RAY DIFFRACTION99
2.0457-2.11170.24941560.22942656X-RAY DIFFRACTION99
2.1117-2.18710.21211470.19952697X-RAY DIFFRACTION100
2.1871-2.27450.24831630.21422626X-RAY DIFFRACTION99
2.2745-2.37790.21051310.19882732X-RAY DIFFRACTION100
2.3779-2.5030.22721260.19842679X-RAY DIFFRACTION99
2.503-2.65950.21971430.19252719X-RAY DIFFRACTION100
2.6595-2.86420.24741580.19742699X-RAY DIFFRACTION100
2.8642-3.15140.21551420.19842743X-RAY DIFFRACTION100
3.1514-3.6050.21861460.18072740X-RAY DIFFRACTION100
3.605-4.53270.18741510.15722753X-RAY DIFFRACTION100
4.5327-19.66490.20571370.18162891X-RAY DIFFRACTION99

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