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- PDB-1qgw: CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYT... -

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Basic information

Entry
Database: PDB / ID: 1qgw
TitleCRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYTE RHODOMONAS CS24
Components
  • (PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA- ...) x 2
  • PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
KeywordsPHOTOSYNTHESIS / PHYCOERYTHRIN / LIGHT-HARVESTING PROTEIN / CRYPTOPHYTE / PHYCOBILIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsHarrop, S.J. / Wilk, K.E. / Hiller, R.G. / Curmi, P.M.G.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Phycobilins of Cryptophycean Algae. Occurance of Dihydrobiliverdin and Mesobiliverdin in Cryptomonad Biliproteins.
Authors: Wedemayer, G.J. / Kidd, D.G. / Wemmer, D.E. / Glazer, A.N.
History
DepositionMay 10, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.source
Revision 1.4Dec 21, 2022Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.5Sep 20, 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
A: PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN))
B: PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN))
C: PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
D: PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,04115
Polymers52,2554
Non-polymers4,78611
Water15,223845
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22500 Å2
ΔGint-205 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.030, 82.630, 89.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9059, -0.352, 0.2354), (-0.3661, 0.3719, -0.853), (0.2128, -0.8589, -0.4658)3.614, 42.077, 64.811
2given(-0.8778, -0.3985, 0.2657), (-0.4162, 0.3601, -0.8349), (0.237, -0.8435, -0.482)3.53, 42.991, 64.362

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Components

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PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA- ... , 2 types, 2 molecules AB

#1: Protein PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN))


Mass: 8135.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA
Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: Q00433
#2: Protein PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN))


Mass: 7042.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA
Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: Q00433, UniProt: P30943*PLUS

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Protein , 1 types, 2 molecules CD

#3: Protein PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))


Mass: 18539.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CSIRO DIVISION OF FISHERIES HOBART TASMAINIA AUSTRALIA
Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Cellular location: THYLAKOID LUMEN / Strain: CS 24 / References: UniProt: P27198

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Non-polymers , 5 types, 856 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.: 845 / 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: 44.86 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
2100 mM1reservoirMgCl2
350 mM1reservoirLiCl
450 mMTris1reservoir
520 mg/mlprotain1drop
650 mMMES1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. obs: 264395 / % possible obs: 95.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 21.3
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 12 / Rsym value: 0.104 / % possible all: 79.4
Reflection
*PLUS
Num. obs: 56582 / Num. measured all: 264395
Reflection shell
*PLUS
% possible obs: 79.4 % / Mean I/σ(I) obs: 12

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Processing

Software
NameClassification
AMoREphasing
ARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BETA CHAIN FROM PDB ENTRY 1LIA

1lia


Resolution: 1.63→20 Å / SU B: 1.506 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1697 3 %RANDOM
Rwork0.149 ---
obs-56582 95.4 %-
Displacement parametersBiso mean: 8.2 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 359 833 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0190.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.822
X-RAY DIFFRACTIONp_mcangle_it1.183
X-RAY DIFFRACTIONp_scbond_it1.222
X-RAY DIFFRACTIONp_scangle_it1.813
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 8.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_mcbond_it20.82
X-RAY DIFFRACTIONp_scbond_it21.22
X-RAY DIFFRACTIONp_mcangle_it31.18
X-RAY DIFFRACTIONp_scangle_it31.81

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