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- PDB-2x21: Structure of Peridinin-Chlorophyll-Protein reconstituted with BChl-a -

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Basic information

Entry
Database: PDB / ID: 2x21
TitleStructure of Peridinin-Chlorophyll-Protein reconstituted with BChl-a
ComponentsPERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC
KeywordsPHOTOSYNTHESIS / LIGHT-HARVESTING POLYPEPTIDE / LIGHT HARVESTING PROTEIN / ALPHA HELICAL / CHROMOPHORE / CHLOROPLAST / CAROTENOIDS
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
BACTERIOCHLOROPHYLL A / : / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / DI(HYDROXYETHYL)ETHER / PERIDININ / Peridinin-chlorophyll a-binding protein 1, chloroplastic
Similarity search - Component
Biological speciesAMPHIDINIUM CARTERAE (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchulte, T. / Hiller, R.G. / Hofmann, E.
CitationJournal: FEBS Lett. / Year: 2010
Title: X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls.
Authors: Schulte, T. / Hiller, R.G. / Hofmann, E.
History
DepositionJan 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 2, 2026Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_nonpoly_atom_coordination ...pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,65927
Polymers15,9541
Non-polymers5,70526
Water4,270237
1
M: PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC
hetero molecules

M: PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,31854
Polymers31,9082
Non-polymers11,40952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area24310 Å2
ΔGint-356 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 81.810, 74.980
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-2224-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules M

#1: Protein PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC / PCP


Mass: 15954.204 Da / Num. of mol.: 1 / Fragment: RESIDUES 57-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMPHIDINIUM CARTERAE (eukaryote) / Strain: CS-21 / Plasmid: PND707 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P80484
#4: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 8 types, 262 molecules

#2: Chemical ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#3: Chemical
ChemComp-PID / PERIDININ


Mass: 630.810 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H50O7
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 42.99 % / Description: NONE
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: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 2, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→43.01 Å / Num. obs: 21555 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

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

3iis


Resolution: 1.75→43.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.738 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1079 5 %RANDOM
Rwork0.146 ---
obs0.148 20476 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 342 237 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0211513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.7112.2262098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6225156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78526.36444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21915200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.046152
X-RAY DIFFRACTIONr_chiral_restr0.2930.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0211102
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_it1.3821.5766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09421220
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4493747
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8934.5864
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 80 -
Rwork0.23 1500 -
obs--100 %

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