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- PDB-4p5r: Structure of oxidized W45Y mutant of amicyanin -

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Basic information

Entry
Database: PDB / ID: 4p5r
TitleStructure of oxidized W45Y mutant of amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / Type-I blue copper protein / Beta sandwich
Function / homology
Function and homology information


electron transfer activity / periplasmic space / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsSukumar, N. / Davidson, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: The sole tryptophan of amicyanin enhances its thermal stability but does not influence the electronic properties of the type 1 copper site.
Authors: Dow, B.A. / Sukumar, N. / Matos, J.O. / Choi, M. / Schulte, A. / Tatulian, S.A. / Davidson, V.L.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.id ..._chem_comp.formula / _chem_comp.id / _chem_comp.name / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5693
Polymers11,4821
Non-polymers872
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.147, 56.146, 28.688
Angle α, β, γ (deg.)90.000, 95.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amicyanin /


Mass: 11482.135 Da / Num. of mol.: 1 / Fragment: UNP residues 27-131 / Mutation: W45Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: mauC, ami / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22364
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.89 Å3/Da / Density % sol: 35.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Initial crystals were obtained from Hampton research ammonium sulfate screen (HR2-211). Bigger crystals grown by macro-seeding using 3.2M Na/K phosphate solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.09→25.439 Å / Num. obs: 33282 / % possible obs: 93.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Χ2: 1.037 / Net I/av σ(I): 31.825 / Net I/σ(I): 12.8 / Num. measured all: 225605
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.09-1.1360.11627910.97678
1.13-1.176.90.09732611.09592
1.17-1.2370.08332811.02692.8
1.23-1.2970.07733591.0593.5
1.29-1.3770.06933481.02194.3
1.37-1.4870.06233770.97595.4
1.48-1.636.90.05634251.05495.8
1.63-1.866.90.05834541.01996.9
1.86-2.356.70.04535141.09697.8
2.35-506.30.03834721.04495.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→25.439 Å / SU ML: 0.07 / σ(F): 1.44 / Phase error: 12.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1535 1661 4.99 %
Rwork0.1273 31597 -
obs0.1286 33258 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 27.69 Å2 / Biso mean: 8.1898 Å2 / Biso min: 3.55 Å2
Refinement stepCycle: final / Resolution: 1.09→25.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 2 171 978
Biso mean--7.8 15.17 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016862
X-RAY DIFFRACTIONf_angle_d1.8211175
X-RAY DIFFRACTIONf_chiral_restr0.106134
X-RAY DIFFRACTIONf_plane_restr0.012151
X-RAY DIFFRACTIONf_dihedral_angle_d10.922326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0899-1.12190.15791100.10912105221575
1.1219-1.15820.11721380.09242562270091
1.1582-1.19950.13311350.09132619275492
1.1995-1.24760.12551390.09972646278593
1.2476-1.30430.14381410.10212614275594
1.3043-1.37310.13231450.10722667281295
1.3731-1.45910.14331370.10552671280895
1.4591-1.57180.14651400.11082707284796
1.5718-1.72990.14171510.1212735288696
1.7299-1.98020.14561370.13922752288997
1.9802-2.49450.19971490.14582787293698
2.4945-25.44630.16321390.15652732287195

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