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- PDB-1xg0: High resolution crystal structure of phycoerythrin 545 from the m... -

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Basic information

Entry
Database: PDB / ID: 1xg0
TitleHigh resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24
Components
  • (Phycoerythrin alpha- ...) x 2
  • B-phycoerythrin beta chain
KeywordsPHOTOSYNTHESIS / PHYCOERYTHRIN / LIGHT-HARVESTING PROTEIN / CRYPTOPHYTE
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A / Phycoerythrin alpha chain / Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit ...Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A / Phycoerythrin alpha chain / Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Globin-like / Globin-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
15,16-DIHYDROBILIVERDIN / PHYCOERYTHROBILIN / B-phycoerythrin beta chain / Phycoerythrin alpha-2 chain, chloroplastic / Phycoerythrin alpha-3 chain, chloroplastic
Similarity search - Component
Biological speciesRhodomonas sp. CS24 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsDoust, A.B. / Marai, C.N.J. / Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. / Scholes, G.D.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy
Authors: Doust, A.B. / Marai, C.N.J. / Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. / Scholes, G.D.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1999
Title: Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution
Authors: Wilk, K.E. / Harrop, S.J. / Jankova, L. / Edler, D. / Keenan, G. / Sharples, F. / Hiller, R.G. / Curmi, P.M.G.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Phycobilins of cryptophycean algae. Occurrence of dihydrobiliverdin and mesobiliverdin in cryptomonad biliproteins
Authors: Wedemayer, G.J. / Kidd, D.G. / Wemmer, D.E. / Glazer, A.N.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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: Phycoerythrin alpha-3 chain
B: Phycoerythrin alpha-2 chain
C: B-phycoerythrin beta chain
D: B-phycoerythrin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,02615
Polymers52,2404
Non-polymers4,78611
Water18,9521052
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22560 Å2
ΔGint-203 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 82.764, 89.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe Biological assembly is alpha1 aplha2 beta beta hetrodimer.

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Components

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Phycoerythrin alpha- ... , 2 types, 2 molecules AB

#1: Protein Phycoerythrin alpha-3 chain / cryptophytan phycoerythrin (alpha-1 chain)


Mass: 8135.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: Q00433
#2: Protein Phycoerythrin alpha-2 chain / cryptophytan phycoerythrin (alpha-2 chain)


Mass: 7027.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: P30943

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Protein , 1 types, 2 molecules CD

#3: Protein B-phycoerythrin beta chain / cryptophytan phycoerythrin (beta chain)


Mass: 18539.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: P27198

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Non-polymers , 5 types, 1063 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DBV / 15,16-DIHYDROBILIVERDIN


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1052 / 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: 2.23 Å3/Da / Density % sol: 44.88 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.966→60.86 Å / Num. all: 270473 / Num. obs: 249226 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 13.4
Reflection shellResolution: 0.966→1.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.55 / % possible all: 82.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGW

1qgw


Resolution: 0.97→60.86 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.455 / SU ML: 0.011 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.017 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12598 7580 3 %RANDOM
Rwork0.10669 ---
all0.10727 241569 --
obs0.10727 241569 89.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.253 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 0.97→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 359 1040 5126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224152
X-RAY DIFFRACTIONr_bond_other_d0.0010.023711
X-RAY DIFFRACTIONr_angle_refined_deg1.8092.0735672
X-RAY DIFFRACTIONr_angle_other_deg138682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03725.299134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88115677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9171518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
X-RAY DIFFRACTIONr_nbd_refined0.2410.2941
X-RAY DIFFRACTIONr_nbd_other0.1880.23824
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22036
X-RAY DIFFRACTIONr_nbtor_other0.0890.21950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.2110
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.00552699
X-RAY DIFFRACTIONr_mcbond_other1.12351047
X-RAY DIFFRACTIONr_mcangle_it2.56454045
X-RAY DIFFRACTIONr_scbond_it3.19871721
X-RAY DIFFRACTIONr_scangle_it3.975101596
X-RAY DIFFRACTIONr_rigid_bond_restr1.52838382
X-RAY DIFFRACTIONr_sphericity_free10.55331040
X-RAY DIFFRACTIONr_sphericity_bonded3.8337771
LS refinement shellResolution: 0.966→0.978 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.32 251 -
Rwork0.261 7680 -
obs--77.81 %

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