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- PDB-3ie9: Structure of oxidized M98L mutant of amicyanin -

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Basic information

Entry
Database: PDB / ID: 3ie9
TitleStructure of oxidized M98L mutant of amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / TYPE-I BLUE COPPER PROTEIN / BETA SANDWICH / Copper / Metal-binding / Periplasm / Transport
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
ACETATE ION / COPPER (II) ION / PHOSPHATE ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSukumar, N. / Davidson, V.L.
CitationJournal: Biochemistry / Year: 2009
Title: Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine.
Authors: Choi, M. / Sukumar, N. / Liu, A. / Davidson, V.L.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms / software
Item: _audit_author.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.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 1.4Sep 6, 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)11,8066
Polymers11,4871
Non-polymers3185
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amicyanin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)70,83336
Polymers68,9236
Non-polymers1,91130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area8250 Å2
ΔGint-58 kcal/mol
Surface area25550 Å2
MethodPISA
3
A: Amicyanin
hetero molecules

A: Amicyanin
hetero molecules

A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,41718
Polymers34,4613
Non-polymers95515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area1920 Å2
ΔGint-21 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.620, 99.620, 70.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-106-

PO4

21A-108-

ZN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Amicyanin /


Mass: 11487.133 Da / Num. of mol.: 1 / Fragment: residues 27-131 / Mutation: M98L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ami, mauC / Plasmid: pMEG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22364

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Non-polymers , 6 types, 87 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.3808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12438 / % possible obs: 99 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAC

1aac


Resolution: 2.1→50 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.86 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
Details: PO4 CONTAINS TWO OXYGEN ATOMS INSTEAD OF FOUR. IT IS LOCATED ON A TWO-FOLD AXIS AND SYMMETRY GENERATES OTHER TWO OXYGEN ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1198 10.02 %random
Rwork0.185 ---
obs0.188 11953 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.218 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 72.19 Å2 / Biso mean: 37 Å2 / Biso min: 23.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.131 Å20 Å2-0 Å2
2--2.131 Å20 Å2
3----4.262 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 10 82 899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007836
X-RAY DIFFRACTIONf_angle_d1.0051130
X-RAY DIFFRACTIONf_chiral_restr0.07127
X-RAY DIFFRACTIONf_plane_restr0.006146
X-RAY DIFFRACTIONf_dihedral_angle_d15.952294

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