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- PDB-2vjr: The structure of phycocyanin from Gloeobacter violaceus -

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Basic information

Entry
Database: PDB / ID: 2vjr
TitleThe structure of phycocyanin from Gloeobacter violaceus
Components
  • PHYCOCYANIN ALPHA CHAIN
  • PHYCOCYANIN BETA CHAIN
KeywordsPHOTOSYNTHESIS / LIGHT HARVESTING
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
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 chain / Phycocyanin alpha chain
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYCOCYANIN ALPHA CHAIN
B: PHYCOCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9255
Polymers36,1592
Non-polymers1,7663
Water1,51384
1
A: PHYCOCYANIN ALPHA CHAIN
B: PHYCOCYANIN BETA CHAIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)227,54930
Polymers216,95312
Non-polymers10,59618
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area45640 Å2
ΔGint-341.8 kcal/mol
Surface area90480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)117.538, 117.538, 116.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PHYCOCYANIN ALPHA CHAIN


Mass: 17679.852 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: Q7M7F7
#2: Protein PHYCOCYANIN BETA CHAIN


Mass: 18478.953 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: Q7M7C7
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: 33.3 MM LITHIUM SULFATE, 17 MM TRIS HYDROCHLORIDE PH 8.5, 5% W/V PEG 4K, MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION. HANGING DROP VAPOUR DIFFUSION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.283
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.49→29.39 Å / Num. obs: 16967 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 21.11 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.42
Reflection shellResolution: 2.49→2.51 Å / Redundancy: 20.96 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.56 / % possible all: 98.8

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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 1JBO

1jbo


Resolution: 2.6→101.53 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 21.017 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.5 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 766 5.1 %RANDOM
Rwork0.207 ---
obs0.21 14301 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å20 Å2
2---0.52 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 129 84 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222713
X-RAY DIFFRACTIONr_bond_other_d0.0020.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.9822.0193686
X-RAY DIFFRACTIONr_angle_other_deg1.013.0014295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85224.261115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58815430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7631519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023066
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02548
X-RAY DIFFRACTIONr_nbd_refined0.230.2695
X-RAY DIFFRACTIONr_nbd_other0.1940.21852
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21325
X-RAY DIFFRACTIONr_nbtor_other0.0880.21400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.52141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81422640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23531297
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9654.51046
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.418 65
Rwork0.288 1025
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)
13.09930.59870.21051.41360.09091.798-0.0343-0.14390.3810.04970.03430.2478-0.5289-0.408500.22630.15180.02480.1712-0.0433-0.1313-21.046-36.138-22.32
22.2381-1.1190.75521.29030.28421.3546-0.1097-0.19720.06160.1958-0.01790.0719-0.30710.06480.12760.1786-0.0787-0.03170.1221-0.066-0.140711.828-40.923-11.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 162
2X-RAY DIFFRACTION1A1082
3X-RAY DIFFRACTION2B1 - 172
4X-RAY DIFFRACTION2B1082 - 1153

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