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- PDB-4ziz: Serial Femtosecond Crystallography of Soluble Proteins in Lipidic... -

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Basic information

Entry
Database: PDB / ID: 4ziz
TitleSerial Femtosecond Crystallography of Soluble Proteins in Lipidic Cubic Phase (C-Phycocyanin from T. elongatus)
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsELECTRON TRANSPORT / Free electron laser / Phycocyanin / Lipidic cubic phase
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFromme, R. / Ishchenko, A. / Metz, M. / Roy-Chowdhury, S. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C.H. ...Fromme, R. / Ishchenko, A. / Metz, M. / Roy-Chowdhury, S. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C.H. / Weierstall, U. / Liu, W. / Cherezov, V.
CitationJournal: IUCrJ / Year: 2015
Title: Serial femtosecond crystallography of soluble proteins in lipidic cubic phase.
Authors: Fromme, R. / Ishchenko, A. / Metz, M. / Chowdhury, S.R. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C. / Weierstall, U. / Liu, W. / Cherezov, V.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references / Other / Structure summary
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

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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
Water2,990166
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_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area60570 Å2
ΔGint-511 kcal/mol
Surface area66610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.380, 186.380, 60.340
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-309-

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 / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 % / Description: 10 x10x5 um size crystals in total 6,171
Crystal growTemperature: 298 K / Method: batch mode / pH: 7 / Details: 20 mM MgCl2 , 17 %PEG 3,350 / Temp details: LPC jet

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: FEL LPC jet
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.56 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 1.75→31.6 Å / Num. all: 44284 / Num. obs: 44284 / % possible obs: 100 % / Redundancy: 139.4 % / Net I/σ(I): 2.94
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 36.8 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
MOSFLMCrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3l0f

3l0f


Resolution: 1.75→31.561 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1838 4.57 %
Rwork0.2041 --
obs0.2064 40257 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→31.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 43 166 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132674
X-RAY DIFFRACTIONf_angle_d1.7023636
X-RAY DIFFRACTIONf_dihedral_angle_d15.529954
X-RAY DIFFRACTIONf_chiral_restr0.052402
X-RAY DIFFRACTIONf_plane_restr0.006470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79730.50051410.50532952X-RAY DIFFRACTION100
1.7973-1.85020.50171400.43872918X-RAY DIFFRACTION100
1.8502-1.90990.39621400.37582935X-RAY DIFFRACTION100
1.9099-1.97820.31091410.30142943X-RAY DIFFRACTION100
1.9782-2.05740.36481410.30252943X-RAY DIFFRACTION100
2.0574-2.1510.321400.26622933X-RAY DIFFRACTION100
2.151-2.26430.29161410.22772949X-RAY DIFFRACTION100
2.2643-2.40620.28761410.22012944X-RAY DIFFRACTION100
2.4062-2.59190.25961420.19972953X-RAY DIFFRACTION100
2.5919-2.85250.23781410.19782963X-RAY DIFFRACTION100
2.8525-3.26490.24871420.18622958X-RAY DIFFRACTION100
3.2649-4.11210.21811420.15172986X-RAY DIFFRACTION100
4.1121-31.56590.19061460.16683042X-RAY DIFFRACTION100
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)
10.28040.02520.0750.137-0.1410.18220.14370.04240.07450.0435-0.15230.1921-0.0248-0.0745-0.00040.34840.00070.05430.3105-0.01950.338825.34172.9373-5.3403
20.4318-0.6434-0.16791.37830.51110.22620.03590.0879-0.0125-0.0820.0262-0.36890.01910.073300.2902-0.00620.00460.30220.01990.308337.8541-19.5696-6.584
30.08760.03270.06070.1048-0.00860.101-0.11310.2553-0.4566-0.1415-0.07850.06640.5780.34510.00550.3990.0080.04350.291-0.00740.349122.9179-43.474-10.1804
40.953-0.0683-0.23291.7730.10850.29890.0246-0.00750.0892-0.0310.006-0.0164-0.0093-0.0587-0.00060.27070.00120.02280.27140.00260.252230.3362-24.0539-6.1646
50.2547-0.24030.02230.41570.09930.07790.09050.0133-0.13490.4112-0.00830.17770.2198-0.1957-0.00120.3671-0.0544-0.04280.30780.04830.334731.80911.79518.1094
60.37380.1394-0.52690.052-0.19650.7426-0.3792-0.31040.12691.14510.4455-0.51470.5825-0.0613-0.03610.49530.0299-0.18890.32510.00950.549243.15926.169316.8901
71.14170.27950.35030.88340.17160.11640.0764-0.064-0.11490.1611-0.0893-0.1642-0.03240.0078-00.30720.006-0.00120.2453-0.01040.230122.5865-19.795615.1922
80.49550.43810.04940.52380.15410.37220.0031-0.32780.23390.4092-0.03940.08790.0949-0.0411-0.00120.4409-0.01590.03360.3184-0.03360.253120.7887-12.907121.4338
90.32770.07790.18790.50610.03610.26690.0582-0.2348-0.07480.4648-0.1645-0.13780.0420.071900.4215-0.0165-0.060.2823-0.00670.317635.8957-12.318419.8646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 162 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 99 )
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 142 )
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 172 )

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