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- PDB-5mjm: Single-shot pink beam serial crystallography: Phycocyanin (Five c... -

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Basic information

Entry
Database: PDB / ID: 5mjm
TitleSingle-shot pink beam serial crystallography: Phycocyanin (Five chips merged)
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)
Synechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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
Water2,288127
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 area60310 Å2
ΔGint-515 kcal/mol
Surface area68540 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
11B-307-

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)
Variant: BP-1 / 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)
Variant: BP-1 / Strain: BP-1 / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 3 / Mutation: N73X / Source method: isolated from a natural source / Formula: C33H40N4O6 / Source: (natural) Synechococcus elongatus (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: liquid 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 9, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
21.251
ReflectionResolution: 2.3→14.92 Å / Num. obs: 12168 / % possible obs: 68.5 % / Observed criterion σ(F): 3 / Redundancy: 1 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 47.2
Reflection shellResolution: 2.3→2.4 Å / Num. measured obs: 6138 / Num. unique all: 517 / % possible all: 0.23

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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: 2.302→14.917 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 13.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1218 10.05 %Random selection
Rwork0.1385 ---
obs0.1428 12114 66.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→14.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 127 2754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052675
X-RAY DIFFRACTIONf_angle_d0.9033638
X-RAY DIFFRACTIONf_dihedral_angle_d11.21578
X-RAY DIFFRACTIONf_chiral_restr0.037401
X-RAY DIFFRACTIONf_plane_restr0.003472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3015-2.39330.2357400.1499387X-RAY DIFFRACTION21
2.3933-2.50170.2027830.1509664X-RAY DIFFRACTION37
2.5017-2.6330.20491030.1531866X-RAY DIFFRACTION48
2.633-2.79690.18621220.15451070X-RAY DIFFRACTION60
2.7969-3.01120.21181410.16391272X-RAY DIFFRACTION71
3.0112-3.31130.19381610.15221479X-RAY DIFFRACTION81
3.3113-3.78360.17441800.13091626X-RAY DIFFRACTION90
3.7836-4.74140.15341890.11461733X-RAY DIFFRACTION95
4.7414-14.91780.17141990.13491799X-RAY DIFFRACTION96
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)
11.22990.69180.70064.8294-0.36860.5245-0.0617-0.2457-0.6088-0.06870.01180.68720.267-0.1450.0570.227-0.00630.04130.13130.01410.239425.5275-0.109224.5601
26.2075-3.01492.48651.4829-1.42013.2703-0.5235-0.7241-0.58470.5786-0.18030.2104-0.529-0.27570.1830.17630.0753-0.02360.18290.0210.306525.828811.17425.8028
30.104-0.387-0.1062.84790.43220.1040.09090.05880.15950.0918-0.1242-0.46860.0181-0.1789-0.05680.18970.03830.02270.16470.01660.264440.4263-6.041624.1112
44.51263.9581-2.01095.4365-2.28362.76610.0216-0.4243-0.12510.1925-0.0441-0.24210.13510.2177-0.02870.16290.0210.01520.1111-0.01050.226435.0705-37.102723.1938
52.3266-1.62321.72981.2005-0.89362.70020.3287-0.0254-0.3617-0.0421-0.30290.12090.9353-0.1443-0.05930.3167-0.07210.07410.1841-0.05810.25422.6827-43.201419.8189
61.35860.17760.02963.941.76342.1238-0.02170.17810.0955-0.11190.0045-0.30710.0626-0.1631-0.00010.13280.01470.0490.12680.00360.149430.1581-22.985618.6396
70.9807-0.16350.03842.03610.74220.6927-0.0054-0.18520.04250.15170.0039-0.1016-0.0071-0.11170.00730.1460.02980.0030.14650.03790.13230.8763-25.038927.7379
83.4697-1.6148-1.11864.57021.96753.7061-0.05040.44880.1366-0.5538-0.0171-0.0716-0.34260.08780.01220.16180.00260.04050.1527-0.00710.152832.011-11.923112.0392
91.0642-0.0764-0.19131.5664-0.00240.3832-0.02790.09440.2054-0.1379-0.0752-0.40110.0654-0.06120.06180.20970.01190.06760.1332-0.01210.136729.253315.603713.8581
101.6747-0.95670.19431.055-0.08911.1660.20840.1593-0.2517-0.3491-0.18620.2057-0.0063-0.0512-0.01250.210.0266-0.05570.1433-0.02150.178820.537614.070311.9141
111.6746-0.9563-0.19452.4873-0.22961.30850.0150.29260.1318-0.5033-0.0977-0.44140.11140.0564-0.23580.2738-0.01190.07190.1572-0.02190.166236.011812.452510.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 77 )
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 110 )
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 162 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 20 )
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 142 )
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 172 )

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