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- PDB-4dp4: The 1.54 Angstrom crystal structure of reduced (CuI) poplar plast... -

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Basic information

Entry
Database: PDB / ID: 4dp4
TitleThe 1.54 Angstrom crystal structure of reduced (CuI) poplar plastocyanin B at pH 6.0
ComponentsPlastocyanin B, chloroplastic
KeywordsELECTRON TRANSPORT / membrane / thylakoid / transit peptide / plastocyanin-like domain / copper-binding
Function / homology
Function and homology information


: / 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 (I) ION / Plastocyanin B, chloroplastic
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKachalova, G.S. / Shosheva, A.H. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D.
CitationJournal: J.Inorg.Biochem. / Year: 2012
Title: Structural comparison of the poplar plastocyanin isoforms PCa and PCb sheds new light on the role of the copper site geometry in interactions with redox partners in oxygenic photosynthesis.
Authors: Kachalova, G.S. / Shosheva, A.C. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D.
History
DepositionFeb 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
X: Plastocyanin B, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7264
Polymers10,4751
Non-polymers2523
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.913, 46.246, 52.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plastocyanin B, chloroplastic


Mass: 10474.645 Da / Num. of mol.: 1 / Fragment: UNP residues 70-168 / Source method: isolated from a natural source / Source: (natural) Populus nigra (black poplar) / Organelle: chloroplast / Strain: cv. Italica / Tissue: leaf / References: UniProt: P11970
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.85 Å3/Da / Density % sol: 33.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2002 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.54→14.74 Å / Num. all: 11813 / Num. obs: 11778 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 15.01 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.2 / Num. unique all: 584 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PLC

1plc


Resolution: 1.54→14.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.833 / SU ML: 0.063 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23294 560 4.8 %RANDOM
Rwork0.15988 ---
obs0.16317 11187 97.13 %-
all-11517 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0 Å2
2--0.46 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.54→14.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 0 12 124 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02791
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4931.9821075
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08626.76534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45815130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.150.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded4.88851
LS refinement shellResolution: 1.54→1.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 23 -
Rwork0.28 476 -
obs-476 61.68 %

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