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- PDB-2vjh: The structure of Phycoerythrin from Gloeobacter violaceus -

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Basic information

Entry
Database: PDB / ID: 2vjh
TitleThe structure of Phycoerythrin from Gloeobacter violaceus
Components
  • PHYCOERYTHRIN ALPHA CHAIN
  • PHYCOERYTHRIN BETA SUBUNIT
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
PHYCOERYTHROBILIN / PHYCOUROBILIN / Phycoerythrin beta subunit / Phycoerythrin alpha chain
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10, 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 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHYCOERYTHRIN ALPHA CHAIN
B: PHYCOERYTHRIN BETA SUBUNIT
C: PHYCOERYTHRIN ALPHA CHAIN
D: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,16514
Polymers72,2744
Non-polymers5,89110
Water11,385632
1
A: PHYCOERYTHRIN ALPHA CHAIN
B: PHYCOERYTHRIN BETA SUBUNIT
C: PHYCOERYTHRIN ALPHA CHAIN
D: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules

A: PHYCOERYTHRIN ALPHA CHAIN
B: PHYCOERYTHRIN BETA SUBUNIT
C: PHYCOERYTHRIN ALPHA CHAIN
D: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules

A: PHYCOERYTHRIN ALPHA CHAIN
B: PHYCOERYTHRIN BETA SUBUNIT
C: PHYCOERYTHRIN ALPHA CHAIN
D: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,49642
Polymers216,82312
Non-polymers17,67330
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
Buried area44240 Å2
ΔGint-263.9 kcal/mol
Surface area88630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)155.829, 155.829, 155.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 2000
2115C1 - 2000
1125B1 - 2000
2125D1 - 2000

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.31072, -0.81428, 0.4903), (-0.81209, -0.49548, -0.30824), (0.49393, -0.30239, -0.81523)-0.3324, 52.44204, 87.66493
2given(0.31269, -0.81089, 0.49466), (-0.81541, -0.49626, -0.29806), (0.48717, -0.31015, -0.81638)-0.71009, 52.10359, 87.91267

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Components

#1: Protein PHYCOERYTHRIN ALPHA CHAIN


Mass: 17679.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NLD7
#2: Protein PHYCOERYTHRIN BETA SUBUNIT


Mass: 18458.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PASTEUR CULTURE COLLECTION / Source: (natural) GLOEOBACTER VIOLACEUS (bacteria) / Strain: PCC7421 / References: UniProt: Q7NLD6
#3: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-PUB / PHYCOUROBILIN


Mass: 590.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H42N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 10% W/V PEG 8K, 0.33 M SODIUM CACODYLATE, 0.67 M MAGNESIUM CHLORIDE

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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: 2.19→44.99 Å / Num. obs: 64149 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.06 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.53
Reflection shellResolution: 2.19→2.21 Å / Redundancy: 9.23 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.28 / % 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 1B8D

1b8d


Resolution: 2.2→43.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.716 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3239 5.1 %RANDOM
Rwork0.153 ---
obs0.155 60801 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 430 632 6116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225598
X-RAY DIFFRACTIONr_bond_other_d0.0050.023648
X-RAY DIFFRACTIONr_angle_refined_deg2.3282.0637610
X-RAY DIFFRACTIONr_angle_other_deg1.1833.0038848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0585678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59423.366202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0391540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026324
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021158
X-RAY DIFFRACTIONr_nbd_refined0.2070.21215
X-RAY DIFFRACTIONr_nbd_other0.1990.23897
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22677
X-RAY DIFFRACTIONr_nbtor_other0.0920.22593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2469
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.54356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05625346
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98432804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.84.52264
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A964medium positional0.080.5
2B1043medium positional0.080.5
1A1262loose positional0.385
2B1297loose positional0.255
1A964medium thermal0.382
2B1043medium thermal0.382
1A1262loose thermal1.1710
2B1297loose thermal0.6810
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.221 235
Rwork0.167 4408
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)
10.3683-0.0839-0.18480.63780.06350.4632-0.0132-0.00130.01730.01350.01770.01330.04840.0083-0.0045-0.16780.03330.0203-0.15360.0296-0.1351-4.40119.48321.806
20.2805-0.2798-0.15641.29920.72460.56280.0364-0.0388-0.0152-0.04130.0373-0.1307-0.04390.1208-0.0737-0.1084-0.00290.026-0.1053-0.0276-0.10181.71649.99139.518
30.31870.0413-0.11311.12230.69311.1122-0.0046-0.0994-0.01920.21040.0419-0.06910.0960.1297-0.0373-0.04930.03090.0043-0.06050.0244-0.108-6.87439.66661.829
40.58780.15980.31140.79490.21550.8992-0.0224-0.1053-0.04250.0850.01920.07190.0854-0.08530.0032-0.05150.01730.044-0.08530.0469-0.0724-21.16514.12440.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION1A1082 - 1139
3X-RAY DIFFRACTION2B1 - 177
4X-RAY DIFFRACTION2B1050 - 1158
5X-RAY DIFFRACTION3C1 - 164
6X-RAY DIFFRACTION3C1082 - 1139
7X-RAY DIFFRACTION4D1 - 177
8X-RAY DIFFRACTION4D1050 - 1158

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