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- PDB-1ha7: STRUCTURE OF A LIGHT-HARVESTING PHYCOBILIPROTEIN, C-PHYCOCYANIN F... -

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Basic information

Entry
Database: PDB / ID: 1ha7
TitleSTRUCTURE OF A LIGHT-HARVESTING PHYCOBILIPROTEIN, C-PHYCOCYANIN FROM SPIRULINA PLATENSIS AT 2.2A RESOLUTION
Components
  • C-PHYCOCYANIN ALPHA CHAIN
  • C-PHYCOCYANIN BETA CHAIN
KeywordsPHOTOSYNTHESIS / CYANOBACTERIA / LIGHT-HARVESTING PROTEIN / PIGMENT PROTEIN / PHYCOCYANOBILIN / CHROMOPHORE
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 / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesSPIRULINA PLATENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPadyana, A.K. / Rajashankar, K.R. / Ramakumar, S.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2001
Title: Crystal Structure of a Light-Harvesting Protein C-Phycocyanin from Spirulina Platensis
Authors: Padyana, A.K. / Bhat, V.B. / Madyastha, K.M. / Rajashankar, K.R. / Ramakumar, S.
#1: Journal: Biophys.J. / Year: 1999
Title: Crystal Structure of C-Phycocyanin from Cyanidium Caldarium Provides a New Perspective on Phycobilisome Assembly
Authors: Stec, B. / Troxler, R.F. / Teeter, M.M.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Isolation, Crystallization, Crystal Structure Analysis and Refinement of Constitutive C-Phycocyanin from the Chromatically Adapting Cyanobacterium Fremyella Diplosiphon at 1.66 Angstrom Resolution
Authors: Duerring, M. / Schmidt, G.B. / Huber, R.
History
DepositionMar 29, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: C-PHYCOCYANIN ALPHA CHAIN
B: C-PHYCOCYANIN BETA CHAIN
C: C-PHYCOCYANIN ALPHA CHAIN
D: C-PHYCOCYANIN BETA CHAIN
E: C-PHYCOCYANIN ALPHA CHAIN
F: C-PHYCOCYANIN BETA CHAIN
G: C-PHYCOCYANIN ALPHA CHAIN
H: C-PHYCOCYANIN BETA CHAIN
I: C-PHYCOCYANIN ALPHA CHAIN
J: C-PHYCOCYANIN BETA CHAIN
K: C-PHYCOCYANIN ALPHA CHAIN
L: C-PHYCOCYANIN BETA CHAIN
M: C-PHYCOCYANIN ALPHA CHAIN
N: C-PHYCOCYANIN BETA CHAIN
O: C-PHYCOCYANIN ALPHA CHAIN
P: C-PHYCOCYANIN BETA CHAIN
Q: C-PHYCOCYANIN ALPHA CHAIN
R: C-PHYCOCYANIN BETA CHAIN
S: C-PHYCOCYANIN ALPHA CHAIN
T: C-PHYCOCYANIN BETA CHAIN
U: C-PHYCOCYANIN ALPHA CHAIN
V: C-PHYCOCYANIN BETA CHAIN
W: C-PHYCOCYANIN ALPHA CHAIN
X: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,09060
Polymers428,89724
Non-polymers21,19336
Water41,1282283
1
A: C-PHYCOCYANIN ALPHA CHAIN
B: C-PHYCOCYANIN BETA CHAIN
C: C-PHYCOCYANIN ALPHA CHAIN
D: C-PHYCOCYANIN BETA CHAIN
E: C-PHYCOCYANIN ALPHA CHAIN
F: C-PHYCOCYANIN BETA CHAIN
G: C-PHYCOCYANIN ALPHA CHAIN
H: C-PHYCOCYANIN BETA CHAIN
I: C-PHYCOCYANIN ALPHA CHAIN
J: C-PHYCOCYANIN BETA CHAIN
K: C-PHYCOCYANIN ALPHA CHAIN
L: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,04530
Polymers214,44812
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: C-PHYCOCYANIN ALPHA CHAIN
N: C-PHYCOCYANIN BETA CHAIN
O: C-PHYCOCYANIN ALPHA CHAIN
P: C-PHYCOCYANIN BETA CHAIN
Q: C-PHYCOCYANIN ALPHA CHAIN
R: C-PHYCOCYANIN BETA CHAIN
S: C-PHYCOCYANIN ALPHA CHAIN
T: C-PHYCOCYANIN BETA CHAIN
U: C-PHYCOCYANIN ALPHA CHAIN
V: C-PHYCOCYANIN BETA CHAIN
W: C-PHYCOCYANIN ALPHA CHAIN
X: C-PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,04530
Polymers214,44812
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.200, 115.400, 183.040
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211
Details(ALPHA,BETA)*6-HEXAMER. THERE ARE TWO HEXAMERS WITH TWELVECHAINS EACH, IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.THIS STRUCTURE CONTAINS 36 PHYCOCYANOBILIN CHROMOPHORESDISTRIBUTED IN TWO HEXAMERS WITH 18 EACH IN A HEXAMER. CHROMOPHORES ARE COVALENTLY ATTACHED BY THIOETHER BONDS TOCYSTEINE RESIDUES AT THREE POSITIONS IN A (ALPHA,BETA)-MONOMERAT ALPHA 84, BETA 84 AND BETA 155 POSITIONS RESPECTIVELY.SG ATOM OF CYSTEINE RESIDUE IS COVALENTLY BONDED TO CAC ATOMOF CYC (PHYCOCYANOBILIN CHROMOPHORE).

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Components

#1: Protein
C-PHYCOCYANIN ALPHA CHAIN


Mass: 17618.820 Da / Num. of mol.: 12 / Fragment: ALPHA-CHAIN / Source method: isolated from a natural source / Source: (natural) SPIRULINA PLATENSIS (bacteria) / Cellular location: STROMAL SURFACE, PHYCOBILISOME ROD / References: UniProt: P72509
#2: Protein
C-PHYCOCYANIN BETA CHAIN


Mass: 18122.559 Da / Num. of mol.: 12 / Fragment: BETA-CHAIN / Source method: isolated from a natural source / Source: (natural) SPIRULINA PLATENSIS (bacteria) / Cellular location: STROMAL SURFACE, PHYCOBILISOME ROD / References: UniProt: P72508
#3: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALPHA CHAINS ARE NUMBERED 1 - 174 WITH A NUMBERING GAP. RESIDUES 143 AND 156 ARE CONSECUTIVE ...ALPHA CHAINS ARE NUMBERED 1 - 174 WITH A NUMBERING GAP. RESIDUES 143 AND 156 ARE CONSECUTIVE RESIDUES. BETA CHAINS ARE NUMBERED 1 - 174 WITH A NUMBERING GAP. RESIDUES 72 AND 75 ARE CONSECUTIVE RESIDUES. THE NUMBERING GAPS ARE INTRODUCED BASED ON STRUCTURAL SUPERPOSITION OF BETA CHAIN ON ALPHA CHAIN. THE GAPS IN RESPECTIVE CHAINS INDICATE THE PROBABLE INSERTION REGIONS IN THE TWO EVOLUTIONARILY RELATED CHAINS.

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.8
Details: 23% (W/V) PEG 6000, 10% (V/V) OF ETHANOL, 75 MM OF PHOSPHATE BUFFER (PH 6.8)
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
223 %(w/v)PEG60001reservoir
310 %(v/v)ethanol1reservoir
475 mMphosphate1reservoirpH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 223480 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 1177344
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 97.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPC

1cpc


Resolution: 2.2→22.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 212513.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2074 1 %RANDOM
Rwork0.192 ---
obs0.192 208506 92.4 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.332493 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--3.15 Å20 Å2-3.12 Å2
2--10.3 Å20 Å2
3----7.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30024 0 1548 2283 33855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 323 1 %
Rwork0.255 30856 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CYC_CNS.PARCYC_CNS.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.135
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.262 / Rfactor obs: 0.262

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