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- PDB-2j96: The E-configuration of alfa-Phycoerythrocyanin -

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Basic information

Entry
Database: PDB / ID: 2j96
TitleThe E-configuration of alfa-Phycoerythrocyanin
ComponentsPHYCOERYTHROCYANIN ALPHA CHAIN
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSPORT / Z- TO E-ISOMERIZATION / TRANSPORT / CHROMOPHORE / BILE PIGMENT / PHYCOBILISOME / LIGHT HARVESTING / PHYCOBILIPROTEINS
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
PHYCOVIOLOBILIN / Phycoerythrocyanin alpha chain
Similarity search - Component
Biological speciesMASTIGOCLADUS LAMINOSUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSchmidt, M. / Patel, A. / Zhao, Y. / Reuter, W.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Basis for the Photochemistry of Alfa-Phycoerythrocyanin
Authors: Schmidt, M. / Patel, A. / Zhao, Y. / Reuter, W.
History
DepositionNov 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Non-polymer description / Other / 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.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PHYCOERYTHROCYANIN ALPHA CHAIN
B: PHYCOERYTHROCYANIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3414
Polymers35,1632
Non-polymers1,1772
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.808, 102.598, 32.146
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21A-2067-

HOH

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Components

#1: Protein PHYCOERYTHROCYANIN ALPHA CHAIN / PHYCOERYTHROCYANIN


Mass: 17581.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PHYCOVIOLOBILIN CHROMOPHORE ATTACHED TO CYS84 AND REFINED AS A WHOLE
Source: (natural) MASTIGOCLADUS LAMINOSUS (bacteria) / References: UniProt: P00309
#2: Chemical ChemComp-PVN / PHYCOVIOLOBILIN / Phycoviolobilin, bound form


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


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / pH: 7
Details: 1.2 M KPI PH 7.0,0.2 M MGSO4 AT 18 DEG C ILLUMINATION BY 587 NM CRYSTALLIZATION IN THE DARK

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 53396 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 2.3 / % possible all: 93.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7L

2c7l


Resolution: 2.25→50 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE PVN CHROMOPHORE HAS BEEN ATTACHED TO CYS84 USING RESTRAINTS DERIVED FROM METHIONINE AND REFINED AS IF IT WOULD BE AN AMINO ACID
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 898 4.5 %RANDOM
Rwork0.235 ---
obs0.235 17895 91.9 %-
Solvent computationBsol: 21.1171 Å2 / ksol: 0.300406 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.815 Å20 Å21.749 Å2
2---18.144 Å20 Å2
3---12.329 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 86 326 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01483
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_deg1.68283
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.25→2.33 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 74 5.4 %
Rwork0 1359 -
obs--71.5 %
Xplor fileSerial no: 1 / Param file: PVB_1.PARAM.PAR / Topol file: PVB.TOP.TOP

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