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- PDB-3rym: Structure of Oxidized M98K mutant of Amicyanin -

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Basic information

Entry
Database: PDB / ID: 3rym
TitleStructure of Oxidized M98K mutant of Amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / Type I Blue Copper Protein / Beta Sandwich / metal binding
Function / homology
Function and homology information


periplasmic space / electron transfer activity / 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 ...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
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7039 Å
AuthorsSukumar, N. / Davidson, V.L.
CitationJournal: J.Inorg.Biochem. / Year: 2011
Title: Replacement of the axial copper ligand methionine with lysine in amicyanin converts it to a zinc-binding protein that no longer binds copper.
Authors: Sukumar, N. / Choi, M. / Davidson, V.L.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amicyanin
B: Amicyanin
C: Amicyanin
D: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,40510
Polymers46,0134
Non-polymers3926
Water6,521362
1
A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6343
Polymers11,5031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6343
Polymers11,5031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5031
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.367, 51.668, 56.543
Angle α, β, γ (deg.)105.97, 96.48, 108.35
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 1:105 ) and (not element H) and (not element D)A0
211chain 'B' and (resseq 1:105 ) and (not element H) and (not element D)B0
311chain 'C' and (resseq 1:105 ) and (not element H) and (not element D)C0
411chain 'D' and (resseq 1:105 ) and (not element H) and (not element D)D0

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Components

#1: Protein
Amicyanin


Mass: 11503.155 Da / Num. of mol.: 4 / Mutation: M98K
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M zinc sulphate heptahydrate, 0.1M MES pH 6.5, 25% w/v PEG monomethylether 550, 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: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 39551 / Redundancy: 2.14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.82 / Num. unique all: 3930

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAC

1aac


Resolution: 1.7039→30.285 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1992 5.04 %random
Rwork0.1901 ---
obs0.1915 39490 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.84 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7407 Å2-0.7302 Å20.241 Å2
2--1.2943 Å23.0382 Å2
3---0.4465 Å2
Refinement stepCycle: LAST / Resolution: 1.7039→30.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 6 362 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183316
X-RAY DIFFRACTIONf_angle_d1.64508
X-RAY DIFFRACTIONf_dihedral_angle_d11.91200
X-RAY DIFFRACTIONf_chiral_restr504
X-RAY DIFFRACTIONf_plane_restr0.01580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A808X-RAY DIFFRACTIONPOSITIONAL0.836
12B808X-RAY DIFFRACTIONPOSITIONAL0.836
13C808X-RAY DIFFRACTIONPOSITIONAL0.712
14D808X-RAY DIFFRACTIONPOSITIONAL0.436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7039-1.76480.25531840.22253483X-RAY DIFFRACTION89
1.7648-1.83540.22551870.20313721X-RAY DIFFRACTION96
1.8354-1.91890.24712050.20783773X-RAY DIFFRACTION96
1.9189-2.02010.23981970.18833735X-RAY DIFFRACTION96
2.0201-2.14660.23891810.18983821X-RAY DIFFRACTION97
2.1466-2.31230.21942050.19483778X-RAY DIFFRACTION97
2.3123-2.54490.24571940.2033810X-RAY DIFFRACTION97
2.5449-2.91290.2232080.21293799X-RAY DIFFRACTION98
2.9129-3.66890.2061960.18323827X-RAY DIFFRACTION98
3.6689-30.29020.182350.15913751X-RAY DIFFRACTION97

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