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- PDB-2c7k: Laue structure of phycoerythrocyanin from Mastigocladus laminosus -

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Basic information

Entry
Database: PDB / ID: 2c7k
TitleLaue structure of phycoerythrocyanin from Mastigocladus laminosus
Components
  • PHYCOERYTHROCYANIN ALPHA CHAIN
  • PHYCOERYTHROCYANIN BETA CHAIN
KeywordsELECTRON TRANSPORT / PHYCOERYTHROCYANIN / PHYCOVIOLOBILIN / PHYCOCYANOBILIN / BILE PIGMENT / CHROMOPHORE / PHOTOSYNTHESIS / PHYCOBILISOME / ANTENNA PROTEIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 Alpha-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 1.1Apr 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 1.2May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.3Dec 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

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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
Water3,351186
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 operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area24770 Å2
ΔGint-210.7 kcal/mol
Surface area40340 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.: 186 / 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: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG, 5MM POTASSIUM PHOSPHATE, PH 8.5, 4 DEG C, 4 MICRO-LITER PROTEIN, HANGING DROP

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50.2 Å / Num. obs: 5868 / % possible obs: 60.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.16
Reflection shellResolution: 3.2→3.4 Å / % possible all: 30.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
LaueViewdata reduction
LaueViewdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7J

2c7j


Resolution: 3.2→50.3 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE CHROMOPHORES WHERE ATTACHED TO THE CYSTEINS USING RESTRAINTS FROM METHIONINE AND TREATED IN THE REFINEMENT AS REGULAR AMINO ACIDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 208 2.2 %RANDOM
Rwork0.192 ---
obs0.192 5868 60.8 %-
Solvent computationBsol: 26.0488 Å2 / ksol: 0.152315 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.465 Å2-1.669 Å20 Å2
2--3.465 Å20 Å2
3----6.929 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.2→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 129 186 2849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006507
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_deg1.24066
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.86
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.002
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: 3.2→3.4 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 -0.5 %
Rwork0.218 458 -
obs--33 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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