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- PDB-4l1e: Crystal structure of C-Phycocyanin from Leptolyngbya sp. N62DM -

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Basic information

Entry
Database: PDB / ID: 4l1e
TitleCrystal structure of C-Phycocyanin from Leptolyngbya sp. N62DM
Components
  • Phycocyanin alpha chain
  • Phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / alpha-beta dimer / light harvesting protein / thylakoid membrane
Function / homology
Function and homology information


: / : / phycobilisome / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / PHYCOCYANOBILIN / Phycocyanin alpha chain / Phycocyanin beta chain
Similarity search - Component
Biological speciesLeptolyngbya sp. N62DM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsSingh, N.K. / Raj, I. / Gourinath, S. / Madamwar, D.
CitationJournal: CNS Neurol Disord Drug Targets / Year: 2014
Title: Crystal Structure and Interaction of Phycocyanin with beta-Secretase: A Putative Therapy for Alzheimer's Disease.
Authors: Singh, N.K. / Hasan, S.S. / Kumar, J. / Raj, I. / Pathan, A.A. / Parmar, A. / Shakil, S. / Gourinath, S. / Madamwar, D.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phycocyanin alpha chain
B: Phycocyanin beta chain
C: Phycocyanin alpha chain
D: Phycocyanin beta chain
E: Phycocyanin alpha chain
F: Phycocyanin beta chain
G: Phycocyanin alpha chain
H: Phycocyanin beta chain
I: Phycocyanin alpha chain
J: Phycocyanin beta chain
K: Phycocyanin alpha chain
L: Phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,61830
Polymers214,10012
Non-polymers10,51818
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61020 Å2
ΔGint-527 kcal/mol
Surface area65640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.467, 107.107, 111.089
Angle α, β, γ (deg.)90.000, 98.270, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 1:162 ) AND (NOT ELEMENT H)
21CHAIN C AND (RESSEQ 1:162 ) AND (NOT ELEMENT H)
12CHAIN B AND (RESSEQ 1:172 ) AND (NOT ELEMENT H)
22CHAIN D AND (RESSEQ 1:172 ) AND (NOT ELEMENT H)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN 'A' AND (RESSEQ 1:162 ) AND (NOT ELEMENT H)A0
211CHAIN 'C' AND (RESSEQ 1:162 ) AND (NOT ELEMENT H)C0
112CHAIN 'B' AND (RESSEQ 1:172 ) AND (NOT ELEMENT H)B0
212CHAIN 'D' AND (RESSEQ 1:172 ) AND (NOT ELEMENT H)D0

NCS ensembles :
ID
1
2

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Components

#1: Protein
Phycocyanin alpha chain


Mass: 17602.820 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. N62DM (bacteria) / References: UniProt: A0A067XG68*PLUS
#2: Protein
Phycocyanin beta chain


Mass: 18080.496 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. N62DM (bacteria) / References: UniProt: A0A067XG69*PLUS
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C33H34N4O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 2000, MgCl2.6H2O,Tris-Cl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2010
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 61840 / % possible obs: 12.91 % / Observed criterion σ(F): 8.19 / Observed criterion σ(I): 11.08 / Biso Wilson estimate: 30.57 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
AUTOMARdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UUM

2uum


Resolution: 2.61→24.978 Å / Occupancy max: 1 / Occupancy min: 0.6 / SU ML: 0.42 / σ(F): 1.4 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 3141 5.08 %
Rwork0.2393 --
obs0.2414 61840 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.8 Å2 / Biso mean: 33.1012 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: LAST / Resolution: 2.61→24.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14946 0 774 244 15964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415996
X-RAY DIFFRACTIONf_angle_d0.92821768
X-RAY DIFFRACTIONf_chiral_restr0.0442380
X-RAY DIFFRACTIONf_plane_restr0.0032802
X-RAY DIFFRACTIONf_dihedral_angle_d16.8765934
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1233X-RAY DIFFRACTIONPOSITIONAL0.075
12C1233X-RAY DIFFRACTIONPOSITIONAL0.075
21B1258X-RAY DIFFRACTIONPOSITIONAL0.042
22D1258X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.65040.3195920.28822061215373
2.6504-2.69380.34211460.27572505265192
2.6938-2.74020.33291330.28372570270391
2.7402-2.790.29121410.27242583272493
2.79-2.84360.32361460.27552606275294
2.8436-2.90150.34391330.27392663279695
2.9015-2.96450.34411230.27492706282996
2.9645-3.03340.31861200.26962695281596
3.0334-3.10910.34621340.28382675280997
3.1091-3.1930.34141540.27292687284197
3.193-3.28670.32371370.27022728286597
3.2867-3.39260.28051420.25812706284897
3.3926-3.51350.30011560.26332735289198
3.5135-3.65380.31711680.24052717288598
3.6538-3.81950.26841600.22822730289098
3.8195-4.02010.26181540.2192728288299
4.0201-4.27080.22291680.2052758292698
4.2708-4.59870.24671780.21142685286398
4.5987-5.0580.2561340.20762781291598
5.058-5.7820.28441430.23082771291499
5.782-7.2550.22711420.23072790293299
7.255-24.9780.20691370.18052819295697
Refinement TLS params.Method: refined / Origin x: -36.9678 Å / Origin y: 24.8881 Å / Origin z: -27.5028 Å
111213212223313233
T0.2404 Å2-0.0123 Å20.0026 Å2-0.2178 Å2-0.0149 Å2--0.2277 Å2
L0.2299 °20.0253 °2-0.0156 °2-0.0607 °2-0.0067 °2--0.0575 °2
S-0.0128 Å °0.0213 Å °-0.0189 Å °-0.0152 Å °0.0117 Å °-0.0261 Å °0.0007 Å °-0.0027 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 1084
2X-RAY DIFFRACTION1ALLB1 - 1153
3X-RAY DIFFRACTION1ALLC1 - 1084
4X-RAY DIFFRACTION1ALLD1 - 1153
5X-RAY DIFFRACTION1ALLE1 - 1084
6X-RAY DIFFRACTION1ALLF1 - 1153
7X-RAY DIFFRACTION1ALLG1 - 1084
8X-RAY DIFFRACTION1ALLH1 - 1153
9X-RAY DIFFRACTION1ALLI1 - 1084
10X-RAY DIFFRACTION1ALLJ1 - 1153
11X-RAY DIFFRACTION1ALLK1 - 1084
12X-RAY DIFFRACTION1ALLL1 - 1153
13X-RAY DIFFRACTION1ALLH - E1 - 324

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