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- PDB-2cj3: CRYSTAL STRUCTURE OF PLASTOCYANIN FROM A CYANOBACTERIUM, ANABAENA... -

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Basic information

Entry
Database: PDB / ID: 2cj3
TitleCRYSTAL STRUCTURE OF PLASTOCYANIN FROM A CYANOBACTERIUM, ANABAENA VARIABILIS
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT / COPPER / TRANSPORT / BETA BARREL / PLASTOCYANIN / METAL-BINDING
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin, cyanobacteria / Plastocyanin / 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 ...Plastocyanin, cyanobacteria / Plastocyanin / 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 / Plastocyanin
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFields, B.A. / Duff, A.P. / Govinderaju, K. / Jackman, M.P. / Lee, H.W. / Church, W.B. / Guss, J.M. / Sykes, A.G. / Freeman, H.C.
CitationJournal: To be Published
Title: The Crystal Structure and Electron-Transfer Reactivity of Plastocyanin from a Cyanobacterium, Anabaena Variabilis
Authors: Fields, B.A. / Duff, A.P. / Govinderaju, K. / Jackman, M.P. / Lee, H.W. / Church, W.B. / Guss, J.M. / Sykes, A.G. / Freeman, H.C.
History
DepositionMar 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Apr 28, 2021Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns ...pdbx_struct_conn_angle / reflns / 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 / _reflns.pdbx_redundancy / _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
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASTOCYANIN
B: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3604
Polymers22,2332
Non-polymers1272
Water1,63991
1
A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1802
Polymers11,1171
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1802
Polymers11,1171
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.290, 68.480, 42.260
Angle α, β, γ (deg.)90.00, 109.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PLASTOCYANIN


Mass: 11116.643 Da / Num. of mol.: 2 / Fragment: HOLOENZYME, RESIDUES 35-139 / Source method: isolated from a natural source / Details: HOLOENZYME, TWO COPIES / Source: (natural) ANABAENA SP. (bacteria) / Strain: PCC 7120 / References: UniProt: P46444
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, HEPES, POTASSIUM PHOSPHATE, SODIUM PHOSPHATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: PHILIPS / Wavelength: 1.5418
DetectorType: NRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Dec 15, 1988 / Details: GRAPHITE MONOCHROMATOR MIRROR AND SI(111)
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. obs: 21041 / % possible obs: 80.1 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.37 / % possible all: 24.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
WEISdata reduction
PROTEINdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PLC

1plc


Resolution: 1.7→39.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.582 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 923 5.1 %RANDOM
Rwork0.14 ---
obs0.141 17228 82.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.17 Å2
2---0.2 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 2 91 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221616
X-RAY DIFFRACTIONr_bond_other_d0.0010.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9822200
X-RAY DIFFRACTIONr_angle_other_deg0.71933424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72425.17258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.936152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.1930.2260
X-RAY DIFFRACTIONr_nbd_other0.1650.21275
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2754
X-RAY DIFFRACTIONr_nbtor_other0.0860.21023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1220.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.62921327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.08231700
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.644649
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1156500
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 37
Rwork0.18 687
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)
10.6003-0.44110.09291.27110.380.8690.0221-0.0052-0.0017-0.02280.0011-0.04680.0057-0.0098-0.0232-0.0176-0.00540.0022-0.01510.0061-0.00715.06761.937121.5231
20.7936-0.35910.1661.16830.24320.74290.0270.0335-0.00310.0589-0.03180.0103-0.0171-0.00010.0048-0.0057-0.00890.0116-0.02260.001-0.0209-0.4267-0.50324.0038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2B1 - 105

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