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- PDB-1pcs: THE 2.15 A CRYSTAL STRUCTURE OF A TRIPLE MUTANT PLASTOCYANIN FROM... -

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Basic information

Entry
Database: PDB / ID: 1pcs
TitleTHE 2.15 A CRYSTAL STRUCTURE OF A TRIPLE MUTANT PLASTOCYANIN FROM THE CYANOBACTERIUM SYNECHOCYSTIS SP. PCC 6803
ComponentsPLASTOCYANIN
KeywordsELECTRON TRANSPORT / PLASTOCYANIN
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 speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRomero, A. / De La Cerda, B. / Varela, P.F. / Navarro, J.A. / Hervas, M. / De La Rosa, M.A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The 2.15 A crystal structure of a triple mutant plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803.
Authors: Romero, A. / De la Cerda, B. / Varela, P.F. / Navarro, J.A. / Hervas, M. / De la Rosa, M.A.
#1: Journal: Biochemistry / Year: 1996
Title: Solution Structure of Reduced Plastocyanin from the Blue-Green Alga Anabaena Variabilis
Authors: Badsberg, U. / Jorgensen, A.M. / Gesmar, H. / Led, J.J. / Hammerstad, J.M. / Jespersen, L.L. / Ulstrup, J.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidized Poplar Plastocyanin at 1.6 A Resolution
Authors: Guss, J.M. / Freeman, H.C.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3952
Polymers10,3321
Non-polymers641
Water1,35175
1
A: PLASTOCYANIN
hetero molecules

A: PLASTOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7904
Polymers20,6632
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)34.300, 34.300, 111.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PLASTOCYANIN


Mass: 10331.574 Da / Num. of mol.: 1 / Mutation: A42D, D47P, A63L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5A / References: UniProt: P21697
#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.: 75 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWHEN SYNECHOCYSTIS PS IS ALIGNED WITH THE AMINO ACID SEQUENCE OF POPLAR PC, THE SEQUENCE OF ...WHEN SYNECHOCYSTIS PS IS ALIGNED WITH THE AMINO ACID SEQUENCE OF POPLAR PC, THE SEQUENCE OF SYNECHOCYSTIS PC HAS TWO ADDITIONAL RESIDUES AT THE N-TERMINAL REGION BUT LACKS THREE AMINO ACIDS IN THE REGION FROM 50 - 61. THUS THE NUMBERING IN SYNECHOCYSTIS PC HAS BEEN CHOSEN IN ACCORDANCE WITH POPLAR PC, WITH THE FIRST TWO RESIDUES NUMBERED AS -2 FOR ALA AND -1 FOR ASN.

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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: 1.94 Å3/Da / Density % sol: 37 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 3.2M AMMONIUM SULFATE, 0.1M NA,K.PHOSPHATE, PH 6.0 WITH A PROTEIN CONCENTRATION OF 10 MG/ML
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMTris-HCl1drop
33.2 Mammonium sulfate1reservoir
40.1 Msodium, potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20.3 Å / Num. obs: 4422 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 12.72 Å2 / Rsym value: 0.065 / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 8.2 / Rsym value: 0.074 / % possible all: 98
Reflection
*PLUS
Num. measured all: 26699 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PCY

1pcy
PDB Unreleased entry


Resolution: 2.15→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 -12 %RANDOM
Rwork0.167 ---
obs0.167 4173 91.6 %-
Displacement parametersBiso mean: 11.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 1 75 803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.627
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.148
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22
X-RAY DIFFRACTIONx_mcangle_it2.52.5
X-RAY DIFFRACTIONx_scbond_it2.52.5
X-RAY DIFFRACTIONx_scangle_it33
LS refinement shellResolution: 2.15→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.269 --
Rwork0.174 644 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSD.PRO
X-RAY DIFFRACTION2PARAM19.SOLAMTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 4070
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.148
LS refinement shell
*PLUS
Rfactor obs: 0.174

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