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- PDB-5owg: Structure of PcyX_EBK42635 -

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Basic information

Entry
Database: PDB / ID: 5owg
TitleStructure of PcyX_EBK42635
ComponentsPcyX_EBK42635
KeywordsOXIDOREDUCTASE / PHYCOBILIN SYNTHESIS / PHYCOERYTHROBILIN / FERREDOXIN DEPENDENT BILIN REDUCTASE / METAGENOMICS
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSommerkamp, J.A. / Ledermann, B. / Frankenberg-Dinkel, N. / Hofmann, E.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationHO2600-3 Germany
German Research FoundationFR1487/10-1 Germany
German-Israeli Foundation of Research and DevelopmentG-1209-276.13/2012
CitationJournal: FEBS J. / Year: 2018
Title: Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages.
Authors: Ledermann, B. / Schwan, M. / Sommerkamp, J.A. / Hofmann, E. / Beja, O. / Frankenberg-Dinkel, N.
History
DepositionSep 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 6, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PcyX_EBK42635


Theoretical massNumber of molelcules
Total (without water)28,3651
Polymers28,3651
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.710, 78.710, 68.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

#1: Protein PcyX_EBK42635


Mass: 28365.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GOS scaffold JCVI_SCAF_1101668336406 / Source: (gene. exp.) marine metagenome (others) / Plasmid: pGEXphipcyX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/HCl pH 8.5, 0.05 M Trimethylamine N-oxide, 15% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2017
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.2→48.45 Å / Num. obs: 24230 / % possible obs: 100 % / Redundancy: 120 % / CC1/2: 1 / Rsym value: 0.213 / Net I/σ(I): 24.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 36.36 % / Mean I/σ(I) obs: 0.51 / Num. unique obs: 1787 / CC1/2: 0.322 / Rsym value: 3.243 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSbuilt 20161205data reduction
XSCALEbuilt 20170601data scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.447 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3184 1225 5.06 %
Rwork0.3023 --
obs0.3032 24211 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 0 13 1505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031526
X-RAY DIFFRACTIONf_angle_d0.5462059
X-RAY DIFFRACTIONf_dihedral_angle_d14.55908
X-RAY DIFFRACTIONf_chiral_restr0.041216
X-RAY DIFFRACTIONf_plane_restr0.003267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.38321310.37042541X-RAY DIFFRACTION100
2.2881-2.39220.44561350.3542551X-RAY DIFFRACTION100
2.3922-2.51830.45571330.34392580X-RAY DIFFRACTION100
2.5183-2.67610.45861390.3452558X-RAY DIFFRACTION100
2.6761-2.88270.38291340.35272531X-RAY DIFFRACTION100
2.8827-3.17280.37641410.33332579X-RAY DIFFRACTION100
3.1728-3.63170.38651350.2982533X-RAY DIFFRACTION100
3.6317-4.5750.2181390.26412560X-RAY DIFFRACTION100
4.575-48.45890.29311380.2912553X-RAY DIFFRACTION100

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