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- PDB-1f56: SPINACH PLANTACYANIN -

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Basic information

Entry
Database: PDB / ID: 1f56
TitleSPINACH PLANTACYANIN
ComponentsPLANTACYANIN
KeywordsPLANT PROTEIN / cupredoxin / copper protein / beta barrel
Function / homology
Function and homology information


: / electron transfer activity
Similarity search - Function
Plantacyanin / Phytocyanin domain / Phytocyanin / Plastocyanin-like domain / Phytocyanin domain profile. / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Plantacyanin / Phytocyanin domain / Phytocyanin / Plastocyanin-like domain / Phytocyanin domain profile. / 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 / Plantacyanin
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsEinsle, O. / Mehrabian, Z. / Nalbandyan, R. / Messerschmidt, A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2000
Title: Crystal structure of plantacyanin, a basic blue cupredoxin from spinach.
Authors: Einsle, O. / Mehrabian, Z. / Nalbandyan, R. / Messerschmidt, A.
History
DepositionJun 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jul 21, 2021Group: Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / refine ...pdbx_struct_conn_angle / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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 / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _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: PLANTACYANIN
B: PLANTACYANIN
C: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,99010
Polymers29,4163
Non-polymers5757
Water3,909217
1
A: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0614
Polymers9,8051
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9653
Polymers9,8051
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9653
Polymers9,8051
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PLANTACYANIN
hetero molecules

C: PLANTACYANIN
hetero molecules

B: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,99010
Polymers29,4163
Non-polymers5757
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area2490 Å2
ΔGint-72 kcal/mol
Surface area14100 Å2
MethodPISA
5
A: PLANTACYANIN
hetero molecules

C: PLANTACYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0267
Polymers19,6102
Non-polymers4155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1040 Å2
ΔGint-49 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.500, 41.832, 158.300
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PLANTACYANIN


Mass: 9805.185 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O82080
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: ammonium sulfate, potassium/sodium tartrate, sodium citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 mMHEPES-NaOH1drop
32.3 Mammonium sulfate1reservoir
40.2 Mpotassium/sodium tartrate1reservoir
50.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. all: 144862 / Num. obs: 15771 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 23.59 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.3
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.383 / Num. unique all: 1184 / % possible all: 87.8
Reflection
*PLUS
Num. measured all: 144862

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.05→25 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.2125 732 4.5 %
Rwork0.1622 --
all-14822 -
obs-14090 85.7 %
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 23 217 2310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007663
X-RAY DIFFRACTIONc_angle_deg1.44093
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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