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- PDB-4yjj: Crystal structure of Phycocyanin from marine cyanobacterium Phorm... -

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Basic information

Entry
Database: PDB / ID: 4yjj
TitleCrystal structure of Phycocyanin from marine cyanobacterium Phormidium rubidum sp. A09DM
Components
  • Alpha Subunit of Cyanobacterial Phycocyanine protein
  • Beta Subunit of Cyanobacterial Phycocyanine protein
KeywordsPHOTOSYNTHESIS / Phycocyanin / Light harvesting Antenna Complex / Phycobillisome
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-Beta subunit / Phycocyanin-Alpha subunit
Similarity search - Component
Biological speciesPhormidium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGupta, G.D. / Kumar, V. / Sonani, R.R. / Madamwar, D.
CitationJournal: To Be Published
Title: Crystal structure of Phycocyanin from marine cyanobacterium Phormidium rubidum sp. A09DM
Authors: Gupta, G.D. / Kumar, V. / Sonani, R.R. / Madamwar, D.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha Subunit of Cyanobacterial Phycocyanine protein
B: Beta Subunit of Cyanobacterial Phycocyanine protein
C: Alpha Subunit of Cyanobacterial Phycocyanine protein
D: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,48210
Polymers70,9504
Non-polymers3,5326
Water1,76598
1
A: Alpha Subunit of Cyanobacterial Phycocyanine protein
B: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules

A: Alpha Subunit of Cyanobacterial Phycocyanine protein
B: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules

A: Alpha Subunit of Cyanobacterial Phycocyanine protein
B: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,72315
Polymers106,4256
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area23950 Å2
ΔGint-257 kcal/mol
Surface area39290 Å2
MethodPISA
2
C: Alpha Subunit of Cyanobacterial Phycocyanine protein
D: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules

C: Alpha Subunit of Cyanobacterial Phycocyanine protein
D: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules

C: Alpha Subunit of Cyanobacterial Phycocyanine protein
D: Beta Subunit of Cyanobacterial Phycocyanine protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,72315
Polymers106,4256
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area23930 Å2
ΔGint-256 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.354, 102.354, 109.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
SymmetryPoint symmetry: (Schoenflies symbol: T (tetrahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 1621 - 162
21SERSERCC1 - 1621 - 162
12ALAALABB1 - 1721 - 172
22ALAALADD1 - 1721 - 172

NCS ensembles :
ID
1
2

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Components

#1: Protein Alpha Subunit of Cyanobacterial Phycocyanine protein


Mass: 17360.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phormidium (bacteria) / References: UniProt: A0A0B6XLG9*PLUS
#2: Protein Beta Subunit of Cyanobacterial Phycocyanine protein


Mass: 18114.537 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phormidium (bacteria) / References: UniProt: A0A0B6XLA1*PLUS
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THE PROTEINS HAVE BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER CEK42834 AND ...THE SEQUENCES OF THE PROTEINS HAVE BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER CEK42834 AND CEK42835 RESPECTIVELY.

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 18.5% PEG 3350, 0.1 M sodium citrate buffer pH 6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54056 Å
DetectorType: AGILENT TITAN CCD / Detector: CCD / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.7→19.34 Å / Num. obs: 17802 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.058 / Net I/σ(I): 12 / Num. measured all: 109336 / Scaling rejects: 356
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.7-2.8340.4213.3950823720.8220.238100
8.96-19.349.30.04542.442264560.9990.01589.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.2.8data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→18 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.845 / WRfactor Rfree: 0.2246 / WRfactor Rwork: 0.1804 / FOM work R set: 0.8317 / SU B: 14.225 / SU ML: 0.29 / SU Rfree: 0.3976 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 908 5.1 %RANDOM
Rwork0.2075 ---
obs0.21 16878 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.61 Å2 / Biso mean: 24.681 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.92 Å2-0 Å2
2---0.92 Å2-0 Å2
3---2.98 Å2
Refinement stepCycle: final / Resolution: 2.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 258 98 5296
Biso mean--23.66 16.04 -
Num. residues----668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025292
X-RAY DIFFRACTIONr_bond_other_d0.0050.025007
X-RAY DIFFRACTIONr_angle_refined_deg2.0832.0257206
X-RAY DIFFRACTIONr_angle_other_deg1.0733.00111444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1475664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34223.679193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42515795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9881532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026084
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021180
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A8794
12C8794
21B9241
22D9241
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 85 -
Rwork0.256 1219 -
all-1304 -
obs--99.92 %

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