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- PDB-5mjq: Single-shot pink beam serial crystallography: Phycocyanin (One chip) -

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Basic information

Entry
Database: PDB / ID: 5mjq
TitleSingle-shot pink beam serial crystallography: Phycocyanin (One chip)
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Phycocyanin / Serial Crystallography / Pink beam
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / 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
PHYCOCYANOBILIN / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeents, A. / Oberthuer, D. / Lieske, J. / Srajer, V. / Sarrou, I.
CitationJournal: Nat Commun / Year: 2017
Title: Pink-beam serial crystallography.
Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / ...Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / Ogata, C.M. / Kissick, D.J. / Taft, M.H. / Manstein, D.J. / Lieske, J. / Oberthuer, D. / Fischetti, R.F. / Chapman, H.N.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4395
Polymers35,6732
Non-polymers1,7663
Water0
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,63630
Polymers214,04012
Non-polymers10,59618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area60570 Å2
ΔGint-516 kcal/mol
Surface area68840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.800, 187.800, 60.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P50032
#2: Protein C-phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 1 / Mutation: N73X / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Mutation: N73X / Source method: isolated from a natural source / Formula: C33H40N4O6

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: liquid diffusion / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.15-1.25
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 9, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
21.251
ReflectionResolution: 2.7→14.918 Å / Num. obs: 6647 / % possible obs: 59.1 % / Observed criterion σ(F): 3 / Redundancy: 1 % / Biso Wilson estimate: 13.5991095346 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 46.56
Reflection shellResolution: 2.7→2.82 Å / % possible all: 0.269

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHASERphasing
Epinormdata reduction
Precognitiondata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBO

1jbo


Resolution: 2.7→14.917 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.62 / Phase error: 15.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 666 10.02 %Random selection
Rwork0.1541 ---
obs0.16 6646 59.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→14.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 0 2627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032675
X-RAY DIFFRACTIONf_angle_d0.7693638
X-RAY DIFFRACTIONf_dihedral_angle_d10.6161578
X-RAY DIFFRACTIONf_chiral_restr0.034401
X-RAY DIFFRACTIONf_plane_restr0.002472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7004-2.90750.2223620.187593X-RAY DIFFRACTION29
2.9075-3.19740.2781040.1782892X-RAY DIFFRACTION45
3.1974-3.65420.23911430.16221284X-RAY DIFFRACTION64
3.6542-4.58160.17921800.13631591X-RAY DIFFRACTION79
4.5816-14.91770.1991770.14761620X-RAY DIFFRACTION78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.07980.02090.02050.47930.25610.13640.0879-0.143-0.0188-0.00170.068-0.1626-0.04840.02260.05920.1478-0.00390.03390.07490.01720.10634.0671-2.226224.4783
20.05980.0236-0.00410.0335-0.03230.04040.0157-0.0337-0.00970.0226-0.0028-0.01780.0004-0.00310.01490.1645-0.05370.08470.074-0.020.129335.5255-36.677423.2343
30.1564-0.0205-0.0860.1046-0.01610.1521-0.04820.0125-0.0599-0.0744-0.087-0.03620.1017-0.0706-0.2207-0.00520.03210.10260.0719-0.0560.0229.4684-26.577723.449
40.00910.0131-0.00570.0134-0.0060.00150.06630.0055-0.0089-0.0303-0.0157-0.0024-0.03240.071800.16830.01780.04510.1213-0.01750.115931.9936-11.850412.0839
50.2448-0.0133-0.16580.0911-0.03990.128-0.10490.0273-0.1137-0.0222-0.0144-0.04670.1366-0.083-0.21070.11590.05890.09990.0744-0.04780.185934.93711.115415.6156
60.15720.12070.02510.2529-0.00160.02510.0076-0.03090.0582-0.0822-0.03680.0741-0.074-0.0267-0.08430.14690.08850.0170.0467-0.00510.050817.421819.62213.827
70.0444-0.0519-0.01430.0863-0.01120.0405-0.01120.03760.0396-0.2148-0.00740.05850.068-0.0982-0.00450.19920.0182-0.04740.1538-0.0190.131227.231613.107810.4378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 162 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 20 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 62 )
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 101 )
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 162 )

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