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- PDB-3dbj: Allophycocyanin from Thermosynechococcus vulcanus -

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Basic information

Entry
Database: PDB / ID: 3dbj
TitleAllophycocyanin from Thermosynechococcus vulcanus
Components(Allophycocyanin) x 2
KeywordsPHOTOSYNTHESIS / phycobilisome / light harvesting / energy transfer / cyanobacteria
Function / homology
Function and homology information


: / : / phycobilisome / photosynthesis
Similarity search - Function
Allophycocyanin, 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 / Allophycocyanin alpha subunit / Allophycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAdir, N. / Klartag, M. / McGregor, A. / David, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Allophycocyanin Trimer Stability and Functionality Are Primarily Due to Polar Enhanced Hydrophobicity of the Phycocyanobilin Binding Pocket
Authors: McGregor, A. / Klartag, M. / David, L. / Adir, N.
History
DepositionJun 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Allophycocyanin
B: Allophycocyanin
C: Allophycocyanin
D: Allophycocyanin
E: Allophycocyanin
F: Allophycocyanin
G: Allophycocyanin
H: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,48916
Polymers139,7798
Non-polymers4,7108
Water6,485360
1
A: Allophycocyanin
B: Allophycocyanin
hetero molecules

A: Allophycocyanin
B: Allophycocyanin
hetero molecules

A: Allophycocyanin
B: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36712
Polymers104,8346
Non-polymers3,5326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20690 Å2
ΔGint-202 kcal/mol
Surface area41660 Å2
MethodPISA
2
C: Allophycocyanin
D: Allophycocyanin
hetero molecules

C: Allophycocyanin
D: Allophycocyanin
hetero molecules

C: Allophycocyanin
D: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36712
Polymers104,8346
Non-polymers3,5326
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 area20710 Å2
ΔGint-202 kcal/mol
Surface area41640 Å2
MethodPISA
3
E: Allophycocyanin
F: Allophycocyanin
hetero molecules

E: Allophycocyanin
F: Allophycocyanin
hetero molecules

E: Allophycocyanin
F: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36712
Polymers104,8346
Non-polymers3,5326
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 area20720 Å2
ΔGint-201 kcal/mol
Surface area41680 Å2
MethodPISA
4
G: Allophycocyanin
H: Allophycocyanin
hetero molecules

G: Allophycocyanin
H: Allophycocyanin
hetero molecules

G: Allophycocyanin
H: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,36712
Polymers104,8346
Non-polymers3,5326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20730 Å2
ΔGint-205 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.597, 102.597, 128.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Allophycocyanin /


Mass: 17555.926 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: B3VNK2
#2: Protein
Allophycocyanin /


Mass: 17388.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: B3VNK3
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% PEG 4000, 400mM MgSO4, 20mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 30684 / % possible obs: 93 % / Redundancy: 2.9 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.7 / % possible all: 88.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ALL

1all


Resolution: 2.9→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 2913 -random
Rwork0.2117 ---
all-33555 --
obs-29023 8.7 %-
Displacement parametersBiso mean: 31.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9744 0 344 360 10448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d19.48
X-RAY DIFFRACTIONc_improper_angle_d0.89

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