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- PDB-5n3u: The structure of the complex of CpcE and CpcF of phycocyanin lyas... -

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Basic information

Entry
Database: PDB / ID: 5n3u
TitleThe structure of the complex of CpcE and CpcF of phycocyanin lyase from Nostoc sp. PCC7120
Components
  • Phycocyanobilin lyase subunit alpha
  • Phycocyanobilin lyase subunit beta
KeywordsLYASE / phycobilisome / chromophorylation / phycocyanin
Function / homology
Function and homology information


Lyases / phycobilisome / lyase activity
Similarity search - Function
PBS lyase HEAT-like repeat / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Phycocyanobilin lyase subunit alpha / Phycocyanobilin lyase subunit beta
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHoeppner, A. / Zhao, C. / Xu, Q.-Z. / Gaertner, W. / Scheer, H. / Zhao, K.-H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F.
Authors: Zhao, C. / Hoppner, A. / Xu, Q.Z. / Gartner, W. / Scheer, H. / Zhou, M. / Zhao, K.H.
History
DepositionFeb 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 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: Phycocyanobilin lyase subunit alpha
B: Phycocyanobilin lyase subunit beta


Theoretical massNumber of molelcules
Total (without water)52,2362
Polymers52,2362
Non-polymers00
Water2,666148
1
A: Phycocyanobilin lyase subunit alpha
B: Phycocyanobilin lyase subunit beta

A: Phycocyanobilin lyase subunit alpha
B: Phycocyanobilin lyase subunit beta


Theoretical massNumber of molelcules
Total (without water)104,4724
Polymers104,4724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10560 Å2
ΔGint-48 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.600, 59.825, 110.634
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Phycocyanobilin lyase subunit alpha / Phycocyanin operon protein CpcE


Mass: 29656.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: cpcE, alr0532 / Production host: Escherichia coli (E. coli) / References: UniProt: P07125, Lyases
#2: Protein Phycocyanobilin lyase subunit beta / Phycocyanin operon protein CpcF


Mass: 22579.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: cpcF, alr0533 / Production host: Escherichia coli (E. coli) / References: UniProt: P29985, Lyases
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.8, 5 % (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.89→57.05 Å / Num. obs: 36870 / % possible obs: 95.3 % / Redundancy: 6.53 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.45
Reflection shellResolution: 1.89→2.01 Å / Mean I/σ(I) obs: 4.53 / Rsym value: 0.494 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC6.5.018refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house structure

Resolution: 1.89→57.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.277 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21616 1813 4.9 %RANDOM
Rwork0.182 ---
obs0.18368 35057 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.06 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.89→57.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 0 148 3449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193374
X-RAY DIFFRACTIONr_bond_other_d0.0020.023350
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9814597
X-RAY DIFFRACTIONr_angle_other_deg1.09437675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16524.507142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81715557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3231523
X-RAY DIFFRACTIONr_chiral_restr0.1280.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1242.9541747
X-RAY DIFFRACTIONr_mcbond_other3.1242.9531746
X-RAY DIFFRACTIONr_mcangle_it4.1164.4132180
X-RAY DIFFRACTIONr_mcangle_other4.1164.4152181
X-RAY DIFFRACTIONr_scbond_it4.2193.4341626
X-RAY DIFFRACTIONr_scbond_other4.2193.4341626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.194.972415
X-RAY DIFFRACTIONr_long_range_B_refined7.20624.2574016
X-RAY DIFFRACTIONr_long_range_B_other7.20524.2674017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 80 -
Rwork0.296 1843 -
obs--67.26 %

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