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- PDB-3iiu: Structure of the reconstituted Peridinin-Chlorophyll a-Protein (R... -

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Basic information

Entry
Database: PDB / ID: 3iiu
TitleStructure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP) mutant N89L
ComponentsPeridinin-chlorophyll a-binding protein 1, chloroplastic
KeywordsPHOTOSYNTHESIS / ALPHA HELICAL / LIGHT HARVESTING PROTEIN / CAROTENOIDS / DINOFLAGELLATES / Chlorophyll / Chloroplast / Chromophore / Light-harvesting polypeptide / Transit peptide
Function / homology
Function and homology information


light-harvesting complex / chlorophyll binding / chloroplast
Similarity search - Function
Peridinin-chlorophyll Protein, Chain M / Peridinin-chlorophyll A binding / Alpha solenoid / Peridinin-chlorophyll A binding protein / Peridinin-chlorophyll A binding superfamily / Peridinin-chlorophyll A binding protein / Mainly Alpha
Similarity search - Domain/homology
: / CHLOROPHYLL A / Chem-J7Z / PERIDININ / Peridinin-chlorophyll a-binding protein 1, chloroplastic
Similarity search - Component
Biological speciesAmphidinium carterae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSchulte, T. / Hofmann, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Identification of a single peridinin sensing Chl-a excitation in reconstituted PCP by crystallography and spectroscopy.
Authors: Schulte, T. / Niedzwiedzki, D.M. / Birge, R.R. / Hiller, R.G. / Polivka, T. / Hofmann, E. / Frank, H.A.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 13, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Peridinin-chlorophyll a-binding protein 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,03116
Polymers15,9531
Non-polymers5,07815
Water5,170287
1
M: Peridinin-chlorophyll a-binding protein 1, chloroplastic
hetero molecules

M: Peridinin-chlorophyll a-binding protein 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,06232
Polymers31,9072
Non-polymers10,15630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area19310 Å2
ΔGint-212 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.510, 81.730, 75.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11M-162-

HOH

21M-369-

HOH

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Components

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Protein , 1 types, 1 molecules M

#1: Protein Peridinin-chlorophyll a-binding protein 1, chloroplastic / PCP


Mass: 15953.259 Da / Num. of mol.: 1 / Fragment: UNP residues 57-207 / Mutation: N89L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphidinium carterae (eukaryote) / Gene: PCP / Plasmid: pND707 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P80484

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Non-polymers , 6 types, 302 molecules

#2: Chemical ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Chemical
ChemComp-PID / PERIDININ / Peridinin


Mass: 630.810 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H50O7
#4: Chemical ChemComp-J7Z / (2S)-3-[(6-O-alpha-D-galactopyranosyl-beta-D-galactopyranosyl)oxy]-2-[(3Z,6Z,9Z,12Z,15Z)-octadeca-3,6,9,12,15-pentaenoyloxy]propyl (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate


Mass: 957.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H80O15
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M CdCl2, 0,1M Sodium Acetate pH 4.6, 20-24% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2008
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.45→43.07 Å / Num. all: 37771 / Num. obs: 37771 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.117 / Net I/σ(I): 16.4
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 11.07 % / Mean I/σ(I) obs: 4.99 / Num. unique all: 6721 / Rsym value: 0.56 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IIS RFPCP

3iis


Resolution: 1.45→43.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.866 / SU ML: 0.034 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17648 1889 5 %RANDOM
Rwork0.15456 ---
all0.15566 37771 --
obs0.15566 37771 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.45→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 326 287 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.2952.2172262
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3685177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44726.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83415234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.163152
X-RAY DIFFRACTIONr_chiral_restr0.240.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211258
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_it0.791.5834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33721344
X-RAY DIFFRACTIONr_scbond_it2.2423792
X-RAY DIFFRACTIONr_scangle_it3.2784.5905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 138 -
Rwork0.222 2614 -
obs--100 %

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