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- PDB-1kdj: OXIDIZED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA -

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Basic information

Entry
Database: PDB / ID: 1kdj
TitleOXIDIZED FORM OF PLASTOCYANIN FROM DRYOPTERIS CRASSIRHIZOMA
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSFER / PHOTOSYSTEM / PAI-PAI STACKING
Function / homology
Function and homology information


electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding
Similarity search - Function
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 speciesAdiantum capillus-veneris (maidenhair fern)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsInoue, T. / Gotowda, M. / Hamada, K. / Kohzuma, T. / Yoshizaki, F. / Sugimura, Y. / Kai, Y.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The structure and unusual pH dependence of plastocyanin from the fern Dryopteris crassirhizoma. The protonation of an active site histidine is hindered by pi-pi interactions.
Authors: Kohzuma, T. / Inoue, T. / Yoshizaki, F. / Sasakawa, Y. / Onodera, K. / Nagatomo, S. / Kitagawa, T. / Uzawa, S. / Isobe, Y. / Sugimura, Y. / Gotowda, M. / Kai, Y.
History
DepositionMay 8, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8502
Polymers10,7861
Non-polymers641
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.118, 73.118, 31.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PLASTOCYANIN


Mass: 10785.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OXIDIZED
Source: (natural) Adiantum capillus-veneris (maidenhair fern)
References: UniProt: Q7SIB8
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium acetate1drop
332 %satammonium sulfate1drop
41 mMsodium azide1reservoir
564-65 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 20, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 10063 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 2.45 / % possible all: 83.3
Reflection
*PLUS
Num. obs: 10220 / % possible obs: 96 % / Num. measured all: 69003 / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POPLAR PLASTOCYANIN

Resolution: 1.7→6 Å / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.255 1016 10 %
Rwork0.234 --
obs0.234 9809 95 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 1 49 808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.78
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.365 117 10 %
Rwork0.34 891 -
obs--83 %
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 9943 / Rfactor obs: 0.241 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75
LS refinement shell
*PLUS
Rfactor Rwork: 0.34

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