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- PDB-5tou: STRUCTURE OF C-PHYCOCYANIN FROM ARCTIC PSEUDANABAENA SP. LW0831 -

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Basic information

Entry
Database: PDB / ID: 5tou
TitleSTRUCTURE OF C-PHYCOCYANIN FROM ARCTIC PSEUDANABAENA SP. LW0831
Components
  • Phycocyanin alpha-1 subunit
  • Phycocyanin beta-1 subunit
KeywordsPHOTOSYNTHESIS / LIGHT-HARVERSTING PIGMENT PROTEIN
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / 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
PHYCOCYANOBILIN / Phycocyanin alpha chain / Phycocyanin beta chain
Similarity search - Component
Biological speciesPseudanabaena sp. lw0831 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsWang, Q.M. / Li, C.Y. / Su, H.N. / Zhang, Y.Z. / Xie, B.B.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structural insights into the cold adaptation of the photosynthetic pigment-protein C-phycocyanin from an Arctic cyanobacterium
Authors: Su, H.N. / Wang, Q.M. / Li, C.Y. / Li, K. / Luo, W. / Chen, B. / Zhang, X.Y. / Qin, Q.L. / Zhou, B.C. / Chen, X.L. / Zhang, Y.Z. / Xie, B.B.
History
DepositionOct 18, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Phycocyanin alpha-1 subunit
D: Phycocyanin beta-1 subunit
A: Phycocyanin alpha-1 subunit
B: Phycocyanin beta-1 subunit
E: Phycocyanin alpha-1 subunit
F: Phycocyanin beta-1 subunit
I: Phycocyanin alpha-1 subunit
J: Phycocyanin beta-1 subunit
G: Phycocyanin alpha-1 subunit
H: Phycocyanin beta-1 subunit
K: Phycocyanin alpha-1 subunit
L: Phycocyanin beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,25430
Polymers210,65712
Non-polymers10,59618
Water30,3191683
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59940 Å2
ΔGint-533 kcal/mol
Surface area66620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.583, 175.718, 194.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phycocyanin alpha-1 subunit


Mass: 17237.242 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudanabaena sp. lw0831 (bacteria) / References: UniProt: V5NXI0
#2: Protein
Phycocyanin beta-1 subunit


Mass: 17872.266 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudanabaena sp. lw0831 (bacteria) / References: UniProt: V5NZF0
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1683 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M SODIUM ACETATE TRIHYDRATE (PH 5.0) AND 18%(W/V) PEG4000 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
PH range: 5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 142799 / % possible obs: 96.7 % / Redundancy: 7 % / Net I/σ(I): 32.04
Reflection shellResolution: 2.04→2.11 Å / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA7

1ha7


Resolution: 2.04→43.93 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.08
RfactorNum. reflection% reflection
Rfree0.207 7048 5.01 %
Rwork0.172 --
obs0.173 140745 95.3 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 32.4 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2803 Å2-0 Å2-0 Å2
2---1.0663 Å20 Å2
3----0.214 Å2
Refinement stepCycle: LAST / Resolution: 2.04→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14738 0 774 1683 17195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01815817
X-RAY DIFFRACTIONf_angle_d1.76921522
X-RAY DIFFRACTIONf_dihedral_angle_d20.9996100
X-RAY DIFFRACTIONf_chiral_restr0.2012394
X-RAY DIFFRACTIONf_plane_restr0.0332730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.042-2.06540.26261830.19983963X-RAY DIFFRACTION85
2.0654-2.08970.27082130.18824030X-RAY DIFFRACTION88
2.0897-2.11520.23682220.17814144X-RAY DIFFRACTION88
2.1152-2.1420.22432400.17774122X-RAY DIFFRACTION91
2.142-2.17020.21441930.18394202X-RAY DIFFRACTION90
2.1702-2.19990.24612120.18074216X-RAY DIFFRACTION92
2.1999-2.23130.22452250.17434251X-RAY DIFFRACTION92
2.2313-2.26460.23142150.1764321X-RAY DIFFRACTION92
2.2646-2.30.23872380.17174311X-RAY DIFFRACTION94
2.3-2.33770.23372210.17194315X-RAY DIFFRACTION92
2.3377-2.3780.20612150.18044413X-RAY DIFFRACTION95
2.378-2.42130.24362310.18074354X-RAY DIFFRACTION94
2.4213-2.46780.22122300.17594452X-RAY DIFFRACTION96
2.4678-2.51820.23252210.17864442X-RAY DIFFRACTION95
2.5182-2.5730.23682670.18184429X-RAY DIFFRACTION97
2.573-2.63280.22582520.17754474X-RAY DIFFRACTION96
2.6328-2.69860.20982320.17654501X-RAY DIFFRACTION97
2.6986-2.77160.20552750.18184522X-RAY DIFFRACTION98
2.7716-2.85310.21542450.17984555X-RAY DIFFRACTION97
2.8531-2.94520.21142350.17754592X-RAY DIFFRACTION98
2.9452-3.05040.20862140.18054642X-RAY DIFFRACTION99
3.0504-3.17250.23872520.18174573X-RAY DIFFRACTION98
3.1725-3.31690.20162430.1764635X-RAY DIFFRACTION99
3.3169-3.49170.20132470.17634651X-RAY DIFFRACTION99
3.4917-3.71040.19882590.15894644X-RAY DIFFRACTION99
3.7104-3.99670.17212400.15674709X-RAY DIFFRACTION99
3.9967-4.39850.18652560.14684704X-RAY DIFFRACTION100
4.3985-5.03420.17852560.15614743X-RAY DIFFRACTION100
5.0342-6.33950.21892580.17824777X-RAY DIFFRACTION99
6.3395-43.93960.17482580.1695010X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -18.6516 Å / Origin y: -16.3828 Å / Origin z: 40.6258 Å
111213212223313233
T0.104 Å20.0065 Å2-0.0033 Å2-0.1408 Å2-0.0104 Å2--0.1453 Å2
L0.0327 °20.0448 °2-0.0152 °2-0.1587 °20.027 °2--0.152 °2
S-0.0077 Å °-0.0078 Å °-0.0005 Å °-0.016 Å °0.0078 Å °-0.0156 Å °0.0012 Å °-0.0036 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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