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- PDB-6jpr: Crystal structure of Phycocyanin from Nostoc sp. R76DM -

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Basic information

Entry
Database: PDB / ID: 6jpr
TitleCrystal structure of Phycocyanin from Nostoc sp. R76DM
Components(Phycocyanin) x 2
KeywordsPHOTOSYNTHESIS / Cyanobacteria / Phycobiliprotein / Light harvesting / Phycocyanobilin
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanins / Phycocyanin, beta subunit / 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 / Phycocyanin
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSonani, R.R. / Gupta, G.D. / Rastogi, R.P. / Patel, S.N. / Madamwar, D. / Kumar, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)PDF.2017.001596 India
CitationJournal: Sci Rep / Year: 2019
Title: Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties.
Authors: Sonani, R.R. / Rastogi, R.P. / Patel, S.N. / Chaubey, M.G. / Singh, N.K. / Gupta, G.D. / Kumar, V. / Madamwar, D.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycocyanin
B: Phycocyanin
C: Phycocyanin
D: Phycocyanin
E: Phycocyanin
F: Phycocyanin
G: Phycocyanin
H: Phycocyanin
I: Phycocyanin
J: Phycocyanin
K: Phycocyanin
L: Phycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,31546
Polymers214,59112
Non-polymers11,72434
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62040 Å2
ΔGint-523 kcal/mol
Surface area66690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.136, 186.158, 85.532
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Phycocyanin


Mass: 17645.738 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: GB MK561022 / Source: (natural) Nostoc (bacteria) / Strain: R76DM / References: UniProt: A0A5H1ZR40*PLUS
#2: Protein
Phycocyanin


Mass: 18119.428 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: GB MK561023 / Source: (natural) Nostoc (bacteria) / Strain: R76DM / References: UniProt: A0A5H1ZR41*PLUS

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Non-polymers , 4 types, 763 molecules

#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAlpha Subunit of Cyanobacterial Phycocyanin protein: GB MK561022, Beta Subunit of Cyanobacterial ...Alpha Subunit of Cyanobacterial Phycocyanin protein: GB MK561022, Beta Subunit of Cyanobacterial Phycocyanin protein: GB MK561023

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.35→46.54 Å / Num. obs: 84711 / % possible obs: 97.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 28.38 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4592 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bv8

2bv8


Resolution: 2.35→37.26 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2481 4113 4.87 %
Rwork0.199 --
obs0.2014 84541 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15120 0 845 729 16694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316276
X-RAY DIFFRACTIONf_angle_d1.09622154
X-RAY DIFFRACTIONf_dihedral_angle_d16.2029532
X-RAY DIFFRACTIONf_chiral_restr0.0362443
X-RAY DIFFRACTIONf_plane_restr0.0032846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37760.32411520.2372813X-RAY DIFFRACTION99
2.3776-2.40660.31281490.23792774X-RAY DIFFRACTION99
2.4066-2.43710.29491340.23272849X-RAY DIFFRACTION99
2.4371-2.46920.29591530.23192758X-RAY DIFFRACTION99
2.4692-2.5030.28521520.22832839X-RAY DIFFRACTION99
2.503-2.53870.29891370.23712728X-RAY DIFFRACTION98
2.5387-2.57660.29911510.23192849X-RAY DIFFRACTION99
2.5766-2.61690.31271550.23032782X-RAY DIFFRACTION98
2.6169-2.65970.31451520.25322760X-RAY DIFFRACTION98
2.6597-2.70560.30551320.25522783X-RAY DIFFRACTION98
2.7056-2.75480.29611520.23612796X-RAY DIFFRACTION98
2.7548-2.80780.3191590.23412799X-RAY DIFFRACTION98
2.8078-2.8650.31511490.23592756X-RAY DIFFRACTION98
2.865-2.92730.30411540.22772793X-RAY DIFFRACTION98
2.9273-2.99540.27341350.21652788X-RAY DIFFRACTION98
2.9954-3.07030.29561210.21392840X-RAY DIFFRACTION98
3.0703-3.15320.30281490.22262771X-RAY DIFFRACTION98
3.1532-3.2460.27681420.21372761X-RAY DIFFRACTION97
3.246-3.35070.24911460.20632784X-RAY DIFFRACTION97
3.3507-3.47030.23741230.21772745X-RAY DIFFRACTION96
3.4703-3.60920.23361360.19592755X-RAY DIFFRACTION97
3.6092-3.77330.24741410.19562689X-RAY DIFFRACTION94
3.7733-3.9720.19431040.19662696X-RAY DIFFRACTION94
3.972-4.22060.18691350.15992769X-RAY DIFFRACTION96
4.2206-4.54590.19991460.15862764X-RAY DIFFRACTION97
4.5459-5.00240.15831600.15992735X-RAY DIFFRACTION97
5.0024-5.7240.21211420.1672769X-RAY DIFFRACTION97
5.724-7.20310.20481400.17642762X-RAY DIFFRACTION97
7.2031-37.26850.19821120.14392721X-RAY DIFFRACTION93

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