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- PDB-7pcy: THE CRYSTAL STRUCTURE OF PLASTOCYANIN FROM A GREEN ALGA, ENTEROMO... -

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Basic information

Entry
Database: PDB / ID: 7pcy
TitleTHE CRYSTAL STRUCTURE OF PLASTOCYANIN FROM A GREEN ALGA, ENTEROMORPHA PROLIFERA
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT PROTEIN
Function / homology
Function and homology information


chloroplast thylakoid membrane / electron transfer activity / 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 speciesUlva prolifera (plant)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsCollyer, C.A. / Guss, J.M. / Freeman, H.C.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Crystal structure of plastocyanin from a green alga, Enteromorpha prolifera.
Authors: Collyer, C.A. / Guss, J.M. / Sugimura, Y. / Yoshizaki, F. / Freeman, H.C.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidized Poplar Plastocyanin at 1.6 Angstroms Resolution
Authors: Guss, J.M. / Freeman, H.C.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Preliminary Crystallographic Data for Plastocyanins from an Alga (Enteromorpha Prolifera) and from Cucumber (Cucumis Sativus)
Authors: Freeman, H.C. / Garrett, T.P.J. / Guss, J.M. / Murata, M. / Yoshizaki, F. / Sugimura, Y. / Shimokoriyama, M.
History
DepositionSep 22, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 6, 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: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1852
Polymers10,1211
Non-polymers641
Water1,892105
1
A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7398
Polymers40,4854
Non-polymers2544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)53.900, 53.900, 59.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Atom site foot note1: RESIDUES PRO 16 AND PRO 36 ARE CIS PROLINES.
2: RESIDUES LYS 4, ASN 18, GLU 43, GLU 59, ASP 61, ASP 85, LYS 93, AND GLN 99 ARE DISORDERED.
3: THERE IS A HYDROGEN BOND BETWEEN OD1 ASP 53 AND OE1(B) GLU 43.
4: SOLVENT MOLECULES 197 - 205 ARE DISORDERED. EACH IS ASSOCIATED WITH A DISORDERED SIDE-CHAIN OR WITH ANOTHER WATER MOLECULE. IN THE LATTER CASE, THE ALTERNATE POSITION IS INDICATED BY *B* IN THE ...4: SOLVENT MOLECULES 197 - 205 ARE DISORDERED. EACH IS ASSOCIATED WITH A DISORDERED SIDE-CHAIN OR WITH ANOTHER WATER MOLECULE. IN THE LATTER CASE, THE ALTERNATE POSITION IS INDICATED BY *B* IN THE ALTERNATE POSITION FIELD OF THE *HETATM* RECORD. SOLVENT MOLECULES LABELLED *B* CORRESPOND TO THOSE MARKED WITH A PRIME IN THE PUBLICATION CITED ON THE *JRNL* RECORDS ABOVE. EACH MEMBER OF A DISORDERED PAIR WAS REFINED WITH OCCUPANCY 0.5.

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Components

#1: Protein PLASTOCYANIN


Mass: 10121.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ulva prolifera (plant) / References: UniProt: P07465
#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.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMsodium pshosphate1reservoir
2ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.85 Å / Num. obs: 3715 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.026

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8.4 Å /
RfactorNum. reflection
obs0.117 5331
Refinement stepCycle: LAST / Resolution: 1.8→8.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 1 111 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.03
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.15
X-RAY DIFFRACTIONp_mcangle_it4.17.5
X-RAY DIFFRACTIONp_scbond_it4.110
X-RAY DIFFRACTIONp_scangle_it5.815
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1320.15
X-RAY DIFFRACTIONp_singtor_nbd0.1550.5
X-RAY DIFFRACTIONp_multtor_nbd0.2090.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.0780.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1920.5
X-RAY DIFFRACTIONp_planar_tor2.35
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 8.4 Å / Num. reflection obs: 5331 / Rfactor obs: 0.117
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg0.18

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