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- PDB-5mjp: Multi-bunch pink beam serial crystallography: Phycocyanin (One chip) -

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Basic information

Entry
Database: PDB / ID: 5mjp
TitleMulti-bunch 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: 2.11 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: 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
Water3,243180
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
Water21612
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 area60650 Å2
ΔGint-517 kcal/mol
Surface area68280 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
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

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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


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Ammonium sulphate

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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 10, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
21.251
ReflectionResolution: 2.106→14.92 Å / Num. obs: 15458 / % possible obs: 64.7 % / Redundancy: 1 % / Biso Wilson estimate: 15.21 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.68
Reflection shellResolution: 2.12→2.22 Å / Num. unique all: 759 / Num. unique obs: 9048 / % possible all: 26.6

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Processing

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

1jbo


Resolution: 2.11→14.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1508 9.85 %Random selection
Rwork0.169 ---
obs0.172 15303 65.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 180 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032698
X-RAY DIFFRACTIONf_angle_d0.8283673
X-RAY DIFFRACTIONf_dihedral_angle_d11.4931599
X-RAY DIFFRACTIONf_chiral_restr0.034404
X-RAY DIFFRACTIONf_plane_restr0.003478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.111-2.1790.1952460.1659391X-RAY DIFFRACTION21
2.179-2.25660.2167810.1745675X-RAY DIFFRACTION36
2.2566-2.34660.2308930.1735886X-RAY DIFFRACTION46
2.3466-2.4530.23261140.17891065X-RAY DIFFRACTION56
2.453-2.58170.21121410.18361243X-RAY DIFFRACTION66
2.5817-2.74250.20811480.18141343X-RAY DIFFRACTION70
2.7425-2.95270.23151530.1871487X-RAY DIFFRACTION77
2.9527-3.24710.22591790.17551605X-RAY DIFFRACTION83
3.2471-3.71060.18421800.15791672X-RAY DIFFRACTION87
3.7106-4.65120.16791970.14671725X-RAY DIFFRACTION89
4.6512-14.89830.19091760.17231703X-RAY DIFFRACTION86
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)
10.8908-0.92720.30774.36080.65060.376-0.0149-0.15750.0223-0.11070.0009-0.1386-0.01960.0690.03110.18780.01730.03030.13040.00220.179733.7173-1.775624.578
25.18366.0256-6.80198.5037-7.03129.4868-0.3370.0546-0.0738-0.09590.0886-0.51310.2489-0.16350.19790.12660.0185-0.00560.1656-0.03220.258338.0203-34.39721.945
32.02240.2817-0.03592.98110.16140.79960.0021-0.0314-0.1065-0.0401-0.0133-0.10090.0486-0.11230.00990.13180.0130.03790.1335-0.00060.09229.4307-27.440923.5996
41.16740.56350.48160.41340.73492.021-0.17370.26060.1531-0.62410.1058-0.5234-0.49450.07480.0570.2752-0.02230.11030.1602-0.01450.36236.6421-9.670512.5666
51.3386-0.8591-0.0032.1387-0.62790.55540.09180.1804-0.0448-0.3732-0.11980.02020.07770.0010.03510.21440.01290.00110.1514-0.03650.122825.088716.187412.5366
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 62 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 63 THROUGH 174 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 33 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 34 THROUGH 174 )

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