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- PDB-1id2: CRYSTAL STRUCTURE OF AMICYANIN FROM PARACOCCUS VERSUTUS (THIOBACI... -

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Basic information

Entry
Database: PDB / ID: 1id2
TitleCRYSTAL STRUCTURE OF AMICYANIN FROM PARACOCCUS VERSUTUS (THIOBACILLUS VERSUTUS)
ComponentsAMICYANIN
KeywordsELECTRON TRANSPORT / Beta Barrel / type-1 blue copper protein / electron transfer protein
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
COPPER (II) ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus versutus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRomero, A. / Nar, H. / Messerschmidt, A.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Crystal structure analysis and refinement at 2.15 A resolution of amicyanin, a type I blue copper protein, from Thiobacillus versutus.
Authors: Romero, A. / Nar, H. / Huber, R. / Messerschmidt, A. / Kalverda, A.P. / Canters, G.W. / Durley, R. / Mathews, F.S.
History
DepositionApr 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.value / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3016
Polymers35,1103
Non-polymers1913
Water2,198122
1
A: AMICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7672
Polymers11,7031
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7672
Polymers11,7031
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AMICYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7672
Polymers11,7031
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.400, 87.400, 38.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe three independent molecules of amicyanin are arranged as columns around 3(2) axes centered at (0, 0) molecule C, (1/3, 2/3) molecule B and (2/3, 1/3) molecule A. The following transformation relate molecule A to B. (-0.975 -0.205 0.081) 49.109 (-0.208 0.977 -0.044) 33.553 (-0.070 -0.060 -0.996) -13.650 A to C: (0.240 -0.970 0.033) 14.988 (-0.969 -0.238 0.052) 49.233 -0.043 -0.044 -0.998) -16.988 C to B: (-0.034 0.999 -0.028) -0.062 (-0.999 -0.034 0.012) 50.335 (0.011 0.028 0.999) 1.745

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Components

#1: Protein AMICYANIN


Mass: 11703.384 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus versutus (bacteria) / Gene: MAUC OR AMI / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P22365
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Reservoir: 2.05 M ammonium sulfate, 0.1 M Na, K phosphate; hanging drop: 5 microliter protein solution (6 mg/ ml) plus 4 microliter 10% (v/v) of MPD and 1.5 microliter 0.5% (v/v) beta-D- ...Details: Reservoir: 2.05 M ammonium sulfate, 0.1 M Na, K phosphate; hanging drop: 5 microliter protein solution (6 mg/ ml) plus 4 microliter 10% (v/v) of MPD and 1.5 microliter 0.5% (v/v) beta-D-glucopyranoside, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
PH range low: 5 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop5 micro litter
310 %(v/v)MPD1drop4 micro litter
40.5 %(v/v)NHG1drop1.5 micro litter
52.05 Mammonium sulfate1reservoir
60.1 MNa, K phosphate1reservoir
2reservoir solution1drop2.5 micro litter

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1993 / Details: Ni-filter
RadiationMonochromator: Ni-Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. all: 92670 / Num. obs: 84144 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.073 / Rsym value: 0.079
Reflection shellResolution: 2.15→2.3 Å / Rmerge(I) obs: 0.345 / Rsym value: 0.383 / % possible all: 72.7
Reflection
*PLUS
Num. obs: 16083 / Num. measured all: 84144
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
PROTEINmodel building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
PROTEINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AAN, these coordinates were supplied by the authors of this entry prior to their release

1aan


Resolution: 2.15→8 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.174 --
all-17603 -
obs-15984 90.8 %
Displacement parametersBiso mean: 24.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 3 122 2588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.36
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rwork: 0.256
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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