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- PDB-2c7l: Low temperature structure of phycoerythrocyanin from Mastigocladu... -

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Basic information

Entry
Database: PDB / ID: 2c7l
TitleLow temperature 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 / MOLECULAR REPLACEMENT / Resolution: 2.85 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 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...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 1.4May 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water7,062392
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
MethodPQS
Unit cell
Length a, b, c (Å)155.000, 155.000, 39.590
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.: 392 / 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: 3.7 Å3/Da / Density % sol: 66 %
Description: ALPHA-BETA STRUCTURE PUBLISHED BY DUERRING ET AL. 1990 WAS USED AS A START
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 4000, 5 MMOL/L POTASSIUM PHOSPHATE, PH 8.5, 4 DEG C, PEC 20 MG/ML, 5 MICO-LITER IN HANGING DROPS

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: SIEMENS / 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: 2.85→39.53 Å / Num. obs: 11512 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 2.85→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.2 / % possible all: 71.8

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Processing

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

Resolution: 2.85→39.5 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE BLA CHROMOPHORES WERE ATTACHED TO CYSTEINS WITH RESTRAINTS ADOPTED FROM METHIONINE AND TREATED IN THE REFINEMENT AS IF THEY WERE REGULAR AMINO ACID RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 576 4.4 %RANDOM
Rwork0.2157 ---
obs0.2157 11511 88 %-
Solvent computationBsol: 10 Å2 / ksol: 0.25227 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.109 Å25.727 Å20 Å2
2---1.109 Å20 Å2
3---2.219 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.85→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 129 392 3055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012006
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_deg1.60953
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
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: 2.85→2.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.243 56 3.5 %
Rwork0.222 1038 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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