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- PDB-2vjt: The Structure of Allophycocyanin from Gloeobacter Violaceus -

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Basic information

Entry
Database: PDB / ID: 2vjt
TitleThe Structure of Allophycocyanin from Gloeobacter Violaceus
Components
  • ALLOPHYCOCYANIN ALPHA SUBUNIT
  • ALLOPHYCOCYANIN BETA SUBUNIT
KeywordsPHOTOSYNTHESIS / LIGHT HARVESTING
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / 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 beta subunit / Allophycocyanin alpha subunit
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMurray, J.W. / Benson, S. / Nield, J. / Barber, J.
CitationJournal: To be Published
Title: The Structures of the Phycobiliproteins of Gloeobacter Violaceus
Authors: Murray, J.W. / Benson, S. / Nield, J. / Barber, J.
History
DepositionDec 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALLOPHYCOCYANIN ALPHA SUBUNIT
B: ALLOPHYCOCYANIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9584
Polymers34,7812
Non-polymers1,1772
Water30617
1
A: ALLOPHYCOCYANIN ALPHA SUBUNIT
B: ALLOPHYCOCYANIN BETA SUBUNIT
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)215,74924
Polymers208,68412
Non-polymers7,06412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area41180 Å2
ΔGint-331.4 kcal/mol
Surface area89760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)164.712, 164.712, 64.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ALLOPHYCOCYANIN ALPHA SUBUNIT


Mass: 17539.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NL80
#2: Protein ALLOPHYCOCYANIN BETA SUBUNIT


Mass: 17241.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NL79
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 30% W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.5→29.45 Å / Num. obs: 11694 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.98 % / Biso Wilson estimate: 40.44 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.41
Reflection shellResolution: 2.5→2.52 Å / Redundancy: 7.07 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.99 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KN1

1kn1


Resolution: 2.5→29.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.199 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.795 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 553 4.7 %RANDOM
Rwork0.196 ---
obs0.2 11691 99.9 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.199 Å2-1.599 Å20 Å2
2---3.199 Å20 Å2
3---4.798 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 86 17 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.912.0243477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33223.564101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94615412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6721519
X-RAY DIFFRACTIONr_chiral_restr0.080.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022878
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2623
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21259
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.52061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81622534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.40731203
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0424.5943
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 10.48→29.2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 9
Rwork0.152 155
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5497-0.5956-0.41041.9039-0.09390.88290.0081-0.2041-0.23250.2188-0.0129-0.36910.07250.18850.00480.16080.021-0.01260.1-0.01250.010733.09718.98825.484
24.6437-0.1694-0.0410.1621-0.16140.2957-0.11660.2869-0.1387-0.10070.07290.04240.0492-0.04820.04360.1114-0.0383-0.01590.08780.01550.061.59427.38313.567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 161
2X-RAY DIFFRACTION1A1081
3X-RAY DIFFRACTION2B1 - 161
4X-RAY DIFFRACTION2B1081

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