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- PDB-2ids: Structure of M98A mutant of amicyanin, Cu(I) -

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Basic information

Entry
Database: PDB / ID: 2ids
TitleStructure of M98A mutant of amicyanin, Cu(I)
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / 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 (I) ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsCarrell, C.J. / Ma, J.K. / Antholine, W. / Hosler, J.P. / Mathews, F.S. / Davidson, V.L.
CitationJournal: Biochemistry / Year: 2007
Title: Generation of Novel Copper Sites by Mutation of the Axial Ligand of Amicyanin. Atomic Resolution Structures and Spectroscopic Properties
Authors: Carrell, C.J. / Ma, J.K. / Antholine, W.E. / Hosler, J.P. / Mathews, F.S. / Davidson, V.L.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)11,5092
Polymers11,4451
Non-polymers641
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.210, 55.100, 26.900
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein Amicyanin /


Mass: 11445.053 Da / Num. of mol.: 1 / Mutation: M98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: mauC, ami / Plasmid: pMEG / Production host: Escherichia coli (E. coli) / References: UniProt: P22364
#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.82 Å3/Da / Density % sol: 32.32 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 3.0 M phosphate, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2005
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. all: 41110 / Num. obs: 71592 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16
Reflection shellResolution: 1→1.02 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.7 / % possible all: 74.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1AAC

1aac


Resolution: 1→30 Å / Num. parameters: 8529 / Num. restraintsaints: 10345 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1695 2051 5 %RANDOM
all0.13 41038 --
obs0.1284 -92.9 %-
Displacement parametersBiso mean: 18.558 Å2
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 790 / Occupancy sum non hydrogen: 938
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 1 133 947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0296
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.037
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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