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- PDB-2q5b: High resolution structure of Plastocyanin from Phormidium laminosum -

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Basic information

Entry
Database: PDB / ID: 2q5b
TitleHigh resolution structure of Plastocyanin from Phormidium laminosum
ComponentsPlastocyanin
KeywordsELECTRON TRANSPORT / Plastocyanin / Photosystem 1
Function / homology
Function and homology information


electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / plasma membrane-derived thylakoid membrane / 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
ACETATE ION / COPPER (II) ION / : / Plastocyanin
Similarity search - Component
Biological speciesPhormidium laminosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFromme, R. / Bukhman-DeRuyter, Y.S. / Grotjohann, I. / Mi, H. / Fromme, P.
CitationJournal: To be Published
Title: Plastocyanin at high resolution from Phormidium laminosum and the double mutant D44A, D45A
Authors: Bukhman-DeRuyter, Y.S. / Fromme, R. / Grotjohann, I. / Schlarb-Ridley, B. / Mi, H. / Fromme, P.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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
B: Plastocyanin
C: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00216
Polymers34,2953
Non-polymers70713
Water4,828268
1
A: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6986
Polymers11,4321
Non-polymers2665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6004
Polymers11,4321
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
3
C: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7046
Polymers11,4321
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-128 kcal/mol
Surface area14040 Å2
MethodPISA
5
C: Plastocyanin
hetero molecules

A: Plastocyanin
hetero molecules

B: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00216
Polymers34,2953
Non-polymers70713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
crystal symmetry operation8_564-y,-x+1,-z-1/21
Buried area2530 Å2
ΔGint-108 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.329, 84.329, 90.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

DetailsThe biological unit is the monomer.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Plastocyanin /


Mass: 11431.800 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phormidium laminosum (bacteria) / Gene: petE / Plasmid: pET11Pc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51883

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Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→42.11 Å / Num. all: 57906 / Num. obs: 57906 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BAW
Resolution: 1.45→9.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.541 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.07
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21017 2920 5.1 %RANDOM
Rwork0.18972 ---
obs0.19075 54607 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.45→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 16 268 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222501
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9583402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.23125.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.742153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021931
X-RAY DIFFRACTIONr_nbd_refined0.2620.21157
X-RAY DIFFRACTIONr_nbtor_refined0.310.21656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.060.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7750.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0440.21
X-RAY DIFFRACTIONr_mcbond_it0.8671.51575
X-RAY DIFFRACTIONr_mcangle_it1.48622548
X-RAY DIFFRACTIONr_scbond_it2.2073938
X-RAY DIFFRACTIONr_scangle_it3.1244.5853
X-RAY DIFFRACTIONr_rigid_bond_restr1.72332513
X-RAY DIFFRACTIONr_sphericity_free2.7393302
X-RAY DIFFRACTIONr_sphericity_bonded2.13832432
LS refinement shellResolution: 1.452→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 190 -
Rwork0.279 3615 -
obs--92.29 %

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