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- PDB-2ov0: Structure of the blue copper protein Amicyanin to 0.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 2ov0
TitleStructure of the blue copper protein Amicyanin to 0.75 A resolution
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / 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 / PHOSPHATE ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.75 Å
AuthorsCarrell, C.J. / Davidson, V.L. / Chen, Z. / Cunane, L.M. / Trickey, P. / Mathews, F.S.
CitationJournal: TO BE PUBLISHED
Title: Ultrahigh resolution studies of amicyanin
Authors: Carrell, C.J. / Davidson, V.L. / Chen, Z. / Cunane, L.M. / Trickey, P. / Mathews, F.S.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6874
Polymers11,5051
Non-polymers1823
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.540, 55.890, 27.160
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amicyanin /


Mass: 11505.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: mauC, ami / Production host: Escherichia coli (E. coli) / 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.87 Å3/Da / Density % sol: 34.31 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 3 M sodium phosphate, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6526 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6526 Å / Relative weight: 1
ReflectionResolution: 0.75→20 Å / Num. all: 105738 / Num. obs: 105738 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.942 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
0.75-0.760.35149990.52593.5
0.76-0.780.3550270.72792.8
0.78-0.790.28251030.58494.9
0.79-0.810.23750610.57494.4
0.81-0.830.20951650.62895.2
0.83-0.840.18251340.71695.9
0.84-0.870.15552010.7996.1
0.87-0.890.13252380.85797.3
0.89-0.920.10553480.91398.9
0.92-0.940.08953410.97399.6
0.94-0.980.07754290.95899.8
0.98-1.020.06753970.84499.9
1.02-1.060.06253670.95499.8
1.06-1.120.05753801.0399.6
1.12-1.190.05154001.5299.7
1.19-1.280.11454010.979100
1.28-1.410.10254090.982100
1.41-1.620.08154261.101100
1.62-2.040.05754421.0999.8
2.04-200.02154701.15899.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO
Starting model: PDB Entry 1AAC

1aac


Resolution: 0.75→20 Å / Num. parameters: 9489 / Num. restraintsaints: 11191 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1418 8437 8 %RANDOM
Rwork0.1251 ---
all0.1263 105709 --
obs0.1251 105709 --
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 794 / Occupancy sum non hydrogen: 1022
Refinement stepCycle: LAST / Resolution: 0.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 7 216 1053
Refine LS restraintsType: s_bond_d / Dev ideal: 0.016

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