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- PDB-4gy3: T. vulcanus Phycocyanin crystallized in 2M Urea -

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Basic information

Entry
Database: PDB / ID: 4gy3
TitleT. vulcanus Phycocyanin crystallized in 2M Urea
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / light harvesting / urea denaturation / globin-type / Photosynthetic antenna / N-methyl asparagine / phycocyanoblilin / membrane attached
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 / UREA / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMarx, A. / Adir, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.
Authors: Marx, A. / Adir, N.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59424
Polymers35,6872
Non-polymers2,90722
Water1,35175
1
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules

A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules

A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,78372
Polymers107,0626
Non-polymers8,72166
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area33760 Å2
ΔGint-203 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.820, 153.820, 39.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein C-phycocyanin alpha subunit


Mass: 17470.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cyanobacterium / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Strain: BP-1 / References: UniProt: Q9AM02
#2: Protein C-phycocyanin beta subunit


Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cyanobacterium / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Strain: BP-1 / References: UniProt: Q71RW8
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH4N2O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 293 K / pH: 8
Details: 0.8M ammonium sulfate, 20mM Tris pH=8 mixed 1:1 with 10mg/ml protein + 2M urea, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→44.4 Å / Num. obs: 18972 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 13

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3018 / Resolution: 2.5→37.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1867 -RANDOM
Rwork0.225 ---
obs0.225 18961 99.9 %-
Displacement parametersBiso mean: 44.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati sigma a0.36 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 205 75 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.32
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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