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- PDB-2c9e: Peridinin-chlorophyll a protein, high-salt form -

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Basic information

Entry
Database: PDB / ID: 2c9e
TitlePeridinin-chlorophyll a protein, high-salt form
ComponentsPERIDININ-CHLOROPHYLL A PROTEIN
KeywordsPHOTOSYNTHESIS / CAROTENOIDS / CHLOROPLAST / LIGHT HARVESTING PROTEIN / LIGHT-HARVESTING POLYPEPTIDE / MULTIGENE FAMILY / TRANSIT PEPTIDE
Function / homology
Function and homology information


light-harvesting complex / : / chlorophyll binding / metal ion binding
Similarity search - Function
Peridinin-chlorophyll A binding protein / Peridinin-chlorophyll A binding superfamily / Peridinin-chlorophyll A binding protein
Similarity search - Domain/homology
CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / PERIDININ / Peridinin-chlorophyll a protein, high-salt form
Similarity search - Component
Biological speciesAMPHIDINIUM CARTERAE (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchulte, T. / Sharples, F.P. / Hiller, R.G. / Hofmann, E.
CitationJournal: Biochemistry / Year: 2009
Title: X-Ray Structure of the High-Salt Form of the Peridinin-Chlorophyll A-Protein from the Dinoflagellate Amphidinium Carterae: Modulation of the Spectral Properties of Pigments by the Protein Environment.
Authors: Schulte, T. / Sharples, F.P. / Hiller, R.G. / Hofmann, E.
History
DepositionDec 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 2.0Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PERIDININ-CHLOROPHYLL A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,18212
Polymers34,6871
Non-polymers7,49511
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.576, 62.673, 63.345
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein PERIDININ-CHLOROPHYLL A PROTEIN


Mass: 34687.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AMPHIDINIUM CARTERAE (eukaryote) / References: UniProt: O76183
#4: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 4 types, 298 molecules

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


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Chemical
ChemComp-PID / PERIDININ / Peridinin


Mass: 630.810 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H50O7
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE IN UNIPROT IS THE RESULT OF CDNA SEQUENCING, THEREFORE SOME RESIDUES IN THE STRUCTURE ...THE SEQUENCE IN UNIPROT IS THE RESULT OF CDNA SEQUENCING, THEREFORE SOME RESIDUES IN THE STRUCTURE DIFFER FROM THE SEQUENCE IN THE DATABASE. MUTATIONS ARE LISTED.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: 8.5 % ISO-PROPANOL, 85 MM HEPES PH 7.5, 17 % PEG 4000, 15 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9198
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 27, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.1→37 Å / Num. obs: 20528 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.8 / % possible all: 87.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPR CHAIN M

1ppr


Resolution: 2.1→36.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1228730.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1027 5 %RANDOM
Rwork0.174 ---
obs0.174 20528 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.726 Å2 / ksol: 0.327842 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.89 Å20 Å21.18 Å2
2--2.58 Å20 Å2
3----7.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-40 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 539 289 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 151 5 %
Rwork0.226 2872 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EPAR_PID-1.CHROMOETOP-NEW_PID.CHROMO

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