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- PDB-2c7j: Phycoerythrocyanin from Mastigocladus laminosus, 295 K, 3.0 A -

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Basic information

Entry
Database: PDB / ID: 2c7j
TitlePhycoerythrocyanin from Mastigocladus laminosus, 295 K, 3.0 A
Components
  • PHYCOERYTHROCYANIN ALPHA CHAIN
  • PHYCOERYTHROCYANIN BETA CHAIN
KeywordsELECTRON TRANSPORT / PHYCOERYTHROCYANIN / PHYCOVIOLOBILIN / PHYCOCYANOBILIN / BILE PIGMENT / CHROMOPHORE / PHOTOSYNTHESIS / PHYCOBILISOME
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
BILIVERDINE IX ALPHA / PHYCOCYANOBILIN / Phycoerythrocyanin alpha chain / Phycoerythrocyanin beta chain
Similarity search - Component
Biological speciesMASTIGOCLADUS LAMINOSUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchmidt, M. / Krasselt, A. / Reuter, W.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: Local Protein Flexibility as a Prerequisite for Reversible Chromophore Isomerization in Alfa- Phycoerythrocyanin
Authors: Schmidt, M. / Krasselt, A. / Reuter, W.
History
DepositionNov 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 1, 2024Group: 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 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8505
Polymers36,0902
Non-polymers1,7603
Water2,684149
1
A: PHYCOERYTHROCYANIN ALPHA CHAIN
B: PHYCOERYTHROCYANIN BETA CHAIN
hetero molecules

A: PHYCOERYTHROCYANIN ALPHA CHAIN
B: PHYCOERYTHROCYANIN BETA CHAIN
hetero molecules

A: PHYCOERYTHROCYANIN ALPHA CHAIN
B: PHYCOERYTHROCYANIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,54915
Polymers108,2696
Non-polymers5,2809
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area25060 Å2
ΔGint-217.1 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.745, 156.745, 40.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PHYCOERYTHROCYANIN ALPHA CHAIN


Mass: 17581.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MASTIGOCLADUS LAMINOSUS (bacteria) / Strain: FISCHERELLA PCC7603 / References: UniProt: P00309
#2: Protein PHYCOERYTHROCYANIN BETA CHAIN


Mass: 18507.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MASTIGOCLADUS LAMINOSUS (bacteria) / Strain: FISCHERELLA PCC7603 / References: UniProt: P00313
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


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


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.8 Å3/Da / Density % sol: 67.5 %
Description: PHYCOERYTHROCYANIN ALFA-BETA PUBLISHED BY DUERRING ET AL. 1992 WAS USED AS A SEARCH MODEL
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 5% PEG 4000, 5 MM POTASSIUM PHOSPHATE, PH 8.5, 4 DEG C, 4 MICRO-LITER OF 20 MG/ML PROTEIN, HANGING DROP

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: SIEMENS, MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→51.3 Å / Num. obs: 9690 / % possible obs: 85.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 61.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SAINTdata reduction
SAINTdata scaling
SCALAdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REMARK

Resolution: 3→51.3 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHROMOPHORES WERE ATTACHED TO CYSTEINS WITH RESTRAINTS DERIVED FROM METHIONINE AND REFINED AS THEY WERE REGULAR AMINO ACIDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1001 8.6 %RANDOM
Rwork0.1894 ---
obs0.1894 9690 83 %-
Solvent computationBsol: 39.8771 Å2 / ksol: 0.270857 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.786 Å2-8.477 Å20 Å2
2--3.786 Å20 Å2
3----7.572 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 129 149 2812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006655
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_deg1.20762
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.05
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.011
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 76 5.3 %
Rwork0.301 613 -
obs--48.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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