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- PDB-4lms: Light harvesting complex PC645 from the cryptophyte Chroomonas sp... -

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Basic information

Entry
Database: PDB / ID: 4lms
TitleLight harvesting complex PC645 from the cryptophyte Chroomonas sp. CCMP270
Components
  • (cryptophyte phycocyanin (alpha- ...) x 2
  • cryptophyte phycocyanin (beta chain)
KeywordsPHOTOSYNTHESIS / thylakoid lumen
Function / homology
Function and homology information


: / : / phycobilisome / chloroplast thylakoid membrane / photosynthesis / chloroplast
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 / Globular protein, non-globular alpha/beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein ...Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A / Phycoerythrin alpha chain / Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Globular protein, non-globular alpha/beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / 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
PHYCOCYANOBILIN / 15,16-DIHYDROBILIVERDIN / mesobiliverdin IX(alpha) / Phycocyanin645 alpha subunit / Phycocyanin645 beta subunit / Phycocyanin645 alpha subunit
Similarity search - Component
Biological speciesChroomonas sp. (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHarrop, S.J. / Wilk, K.E. / Curmi, P.M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins.
Authors: Harrop, S.J. / Wilk, K.E. / Dinshaw, R. / Collini, E. / Mirkovic, T. / Teng, C.Y. / Oblinsky, D.G. / Green, B.R. / Hoef-Emden, K. / Hiller, R.G. / Scholes, G.D. / Curmi, P.M.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: cryptophyte phycocyanin (alpha-1 chain)
B: cryptophyte phycocyanin (beta chain)
C: cryptophyte phycocyanin (alpha-2 chain)
D: cryptophyte phycocyanin (beta chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,31814
Polymers53,0564
Non-polymers5,26210
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22300 Å2
ΔGint-164 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.958, 93.824, 121.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Cryptophyte phycocyanin (alpha- ... , 2 types, 2 molecules AC

#1: Protein cryptophyte phycocyanin (alpha-1 chain)


Mass: 8733.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T880*PLUS
#3: Protein cryptophyte phycocyanin (alpha-2 chain)


Mass: 7558.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T8W5*PLUS

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Protein , 1 types, 2 molecules BD

#2: Protein cryptophyte phycocyanin (beta chain)


Mass: 18381.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T8F2*PLUS

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Non-polymers , 5 types, 774 molecules

#4: Chemical ChemComp-M1V / mesobiliverdin IX(alpha)


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6
#5: Chemical ChemComp-DBV / 15,16-DIHYDROBILIVERDIN


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#6: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG4000, 20% isopropanol, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.821 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 20, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.821 Å / Relative weight: 1
ReflectionResolution: 1.35→17.8 Å / Num. all: 113946 / Num. obs: 109920 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12.3
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.41 / % possible all: 74.6

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: dev_833)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGW

1qgw


Resolution: 1.35→17.038 Å / SU ML: 0.29 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.181 5518 5.02 %RANDOM
Rwork0.1431 ---
obs0.145 109917 96.53 %-
all-109917 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.015 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.475 Å20 Å2-0 Å2
2--1.9232 Å20 Å2
3----3.3982 Å2
Refinement stepCycle: LAST / Resolution: 1.35→17.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 382 764 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013909
X-RAY DIFFRACTIONf_angle_d1.3335285
X-RAY DIFFRACTIONf_dihedral_angle_d16.2891423
X-RAY DIFFRACTIONf_chiral_restr0.07566
X-RAY DIFFRACTIONf_plane_restr0.007666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.30581260.27672561X-RAY DIFFRACTION71
1.3653-1.38140.32861630.24792701X-RAY DIFFRACTION77
1.3814-1.39820.26071370.23272855X-RAY DIFFRACTION80
1.3982-1.41590.28991700.21953036X-RAY DIFFRACTION86
1.4159-1.43450.24151730.2083240X-RAY DIFFRACTION91
1.4345-1.45420.25061650.19393429X-RAY DIFFRACTION95
1.4542-1.4750.2321870.17613486X-RAY DIFFRACTION99
1.475-1.4970.22452150.16393559X-RAY DIFFRACTION99
1.497-1.52030.20551960.15013516X-RAY DIFFRACTION100
1.5203-1.54520.19851780.1423603X-RAY DIFFRACTION100
1.5452-1.57190.17551820.13853541X-RAY DIFFRACTION100
1.5719-1.60040.18441880.14323593X-RAY DIFFRACTION100
1.6004-1.63120.20621930.1343549X-RAY DIFFRACTION100
1.6312-1.66450.18612120.13553605X-RAY DIFFRACTION100
1.6645-1.70060.18971800.13033541X-RAY DIFFRACTION100
1.7006-1.74010.17991780.13063623X-RAY DIFFRACTION100
1.7401-1.78360.22021870.12963585X-RAY DIFFRACTION100
1.7836-1.83180.18182090.12663547X-RAY DIFFRACTION100
1.8318-1.88560.17221870.12743615X-RAY DIFFRACTION100
1.8856-1.94640.18151780.12873615X-RAY DIFFRACTION100
1.9464-2.01590.16061770.13173585X-RAY DIFFRACTION100
2.0159-2.09640.18021850.12723647X-RAY DIFFRACTION100
2.0964-2.19170.15162100.1193592X-RAY DIFFRACTION100
2.1917-2.30690.15061880.1183605X-RAY DIFFRACTION100
2.3069-2.45110.15831920.12043635X-RAY DIFFRACTION100
2.4511-2.63970.1661800.13443672X-RAY DIFFRACTION100
2.6397-2.90420.18171940.14363659X-RAY DIFFRACTION100
2.9042-3.32170.17511920.15023664X-RAY DIFFRACTION100
3.3217-4.17480.17822270.14283697X-RAY DIFFRACTION100
4.1748-17.03950.17021690.15883843X-RAY DIFFRACTION98

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