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- PDB-3ply: Structure of Oxidized P96G Mutant of Amicyanin -

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Basic information

Entry
Database: PDB / ID: 3ply
TitleStructure of Oxidized P96G Mutant of Amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / type-I blue copper protein / beta sandwich / metal-binding
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSukumar, N. / Davidson, V.L.
CitationJournal: Biochemistry / Year: 2011
Title: Proline 96 of the copper ligand loop of amicyanin regulates electron transfer from methylamine dehydrogenase by positioning other residues at the protein-protein interface.
Authors: Choi, M. / Sukumar, N. / Mathews, F.S. / Liu, A. / Davidson, V.L.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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_label_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,39013
Polymers45,8604
Non-polymers5299
Water3,243180
1
A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5754
Polymers11,4651
Non-polymers1103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5292
Polymers11,4651
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7585
Polymers11,4651
Non-polymers2934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5292
Polymers11,4651
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.279, 97.279, 109.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A'
211chain ['B''C''D']

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Amicyanin /


Mass: 11465.108 Da / Num. of mol.: 4 / Fragment: UNP residues 27-131 / Mutation: P96G
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 , 5 types, 189 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8M sodium/potassium phosphate pH 7.5, 40mM ammonium sulfate, 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: 1.14 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30860 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3031

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAC

1aac


Resolution: 2.2→50 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1871 6.46 %random
Rwork0.239 ---
obs0.243 28971 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.425 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.516 Å2-0 Å2-0 Å2
2--1.516 Å20 Å2
3----3.032 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 17 180 3409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083311
X-RAY DIFFRACTIONf_angle_d1.1284499
X-RAY DIFFRACTIONf_dihedral_angle_d13.9481189
X-RAY DIFFRACTIONf_chiral_restr0.077501
X-RAY DIFFRACTIONf_plane_restr0.005578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A804X-RAY DIFFRACTIONPOSITIONAL
12B804X-RAY DIFFRACTIONPOSITIONAL0.058
12C804X-RAY DIFFRACTIONPOSITIONAL0.058
12D804X-RAY DIFFRACTIONPOSITIONAL0.058
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5509-0.0565-0.22192.2059-0.16190.0465-0.5226-0.5717-0.05261.26250.3528-0.05460.2350.24410.10860.8520.30990.04780.24130.02070.104151.1316-4.68-11.7522
20.4695-0.1110.13870.3126-1.08663.7081-0.0490.01880.07870.00840.25310.0553-0.1131-0.4965-0.10940.15870.19260.0937-0.0654-0.0720.045337.475111.4244-28.8751
31.7672-0.22790.87652.99791.78311.66070.1054-0.2083-0.15720.26440.1361-0.45010.3350.1225-0.23530.24140.10490.01340.2619-0.03430.194647.470422.8824-6.6445
40.1484-0.0791-0.12490.84261.01011.2268-0.21150.0433-0.09160.8607-0.58330.36330.9949-0.84190.72940.7698-0.23740.57750.4799-0.21570.229721.98660.6873-7.762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:105)
2X-RAY DIFFRACTION2(chain B and resid 1:105)
3X-RAY DIFFRACTION3(chain C and resid 1:105)
4X-RAY DIFFRACTION4(chain D and resid 1:105)

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