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- PDB-5o7m: Single-shot pink beam serial crystallography: Phycocyanin (One ch... -

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Basic information

Entry
Database: PDB / ID: 5o7m
TitleSingle-shot pink beam serial crystallography: Phycocyanin (One chip, chip_1)
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: 2.46 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
DepositionJun 9, 2017Deposition 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
Water1,20767
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 area60700 Å2
ΔGint-521 kcal/mol
Surface area68060 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
Components on special symmetry positions
IDModelComponents
11B-315-

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 / 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.: 67 / 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: small tubes / pH: 6.4
Details: PC was crystallized in 1.5 M Ammonium Sulfate solution, 25 mM MES pH 6.4. The protein crystals appear overnight in 1 mm inner diameter capillaries. The PC crystals size (30 to 40 um) is ...Details: PC was crystallized in 1.5 M Ammonium Sulfate solution, 25 mM MES pH 6.4. The protein crystals appear overnight in 1 mm inner diameter capillaries. The PC crystals size (30 to 40 um) is correlated to the protein concentration, which varied between 10-15 mg/ml.

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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: 2.46→100 Å / Num. obs: 8931 / % possible obs: 60.02 % / Observed criterion σ(F): 3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 47.57
Reflection shellResolution: 2.46→2.57 Å / Redundancy: 11.83 % / Num. unique obs: 462 / % possible all: 25.16

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Processing

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

1jbo


Resolution: 2.46→14.917 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.55 / Phase error: 14.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 892 10.02 %Same as for 5MJP
Rwork0.142 ---
obs0.1475 8905 59.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→14.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 67 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042675
X-RAY DIFFRACTIONf_angle_d0.833638
X-RAY DIFFRACTIONf_dihedral_angle_d12.0171578
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 (%)
2.4602-2.61360.2251650.1573573X-RAY DIFFRACTION26
2.6136-2.81420.21471020.1615901X-RAY DIFFRACTION41
2.8142-3.09510.21411320.16291166X-RAY DIFFRACTION53
3.0951-3.53770.19961630.14731571X-RAY DIFFRACTION70
3.5377-4.43760.19042110.12371865X-RAY DIFFRACTION84
4.4376-14.91780.17942190.13771937X-RAY DIFFRACTION85
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)
10.1295-0.0659-0.00350.0342-0.01420.3740.0071-0.0048-0.00830.050.0085-0.1659-0.0415-0.0547-0.00220.1066-0.02970.03140.04380.020.174434.0445-2.202824.4657
20.12260.1004-0.00930.105-0.07840.2237-0.0252-0.0785-0.00120.01340.06020.03520.0270.10710.02410.07990.00260.03380.0681-0.03180.136335.4507-36.634523.2185
30.4299-0.2869-0.09170.3464-0.1350.3638-0.122-0.03140.0241-0.0856-0.0761-0.14750.15070.0251-0.87270.07660.02810.0750.0614-0.02530.068429.4465-26.560623.4498
40.14070.01920.09750.00630.03590.2483-0.063-0.0008-0.0253-0.0356-0.07570.1127-0.1012-0.1156-0.28110.20030.0210.10740.0783-0.09130.174731.9442-11.88512.068
50.3828-0.07460.1250.1908-0.07590.4068-0.16490.09170.06230.0275-0.0634-0.11120.0951-0.0637-0.41920.134-0.00610.05560.06330.03290.153534.917111.118315.6076
60.25330.0960.0840.2763-0.16590.19750.103-0.0319-0.0675-0.0803-0.0837-0.06460.0886-0.0917-0.03860.14220.0377-0.05370.0949-0.0260.059317.471719.573513.8151
70.1894-0.26960.08360.4363-0.09880.26680.11480.2045-0.0604-0.2747-0.14540.08440.04810.0299-0.07430.25320.0168-0.01360.1067-0.02010.089827.196513.129210.4548
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 174 )
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 174 )

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