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- PDB-8fwa: Phycocyanin structure from a modular droplet injector for serial ... -

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Basic information

Entry
Database: PDB / ID: 8fwa
TitlePhycocyanin structure from a modular droplet injector for serial femtosecond crystallography
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPLANT PROTEIN / Pigment Protein / Serial femtosecond crystallography / segmented flow injector
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBotha, S. / Doppler, D.L. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. ...Botha, S. / Doppler, D.L. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R. / Karpos, K. / Cruz Villarreal, J. / Nelson, G. / Ketawala, G.K. / Pey, A.L. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Nazari, R. / Sierra, R. / Hunter, M.S. / Batyuk, A. / Kupitz, C.J. / Sublett, R.E. / Lisova, S. / Mariani, V. / Boutet, S. / Fromme, R. / Grant, T.D. / Fromme, P. / Kirian, R.A. / Martin-Garcia, J.M. / Ros, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306, 1565180 United States
CitationJournal: Lab Chip / Year: 2023
Title: Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme.
Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / ...Authors: Doppler, D. / Sonker, M. / Egatz-Gomez, A. / Grieco, A. / Zaare, S. / Jernigan, R. / Meza-Aguilar, J.D. / Rabbani, M.T. / Manna, A. / Alvarez, R.C. / Karpos, K. / Cruz Villarreal, J. / Nelson, G. / Yang, J.H. / Carrion, J. / Morin, K. / Ketawala, G.K. / Pey, A.L. / Ruiz-Fresneda, M.A. / Pacheco-Garcia, J.L. / Hermoso, J.A. / Nazari, R. / Sierra, R. / Hunter, M.S. / Batyuk, A. / Kupitz, C.J. / Sublett, R.E. / Lisova, S. / Mariani, V. / Boutet, S. / Fromme, R. / Grant, T.D. / Botha, S. / Fromme, P. / Kirian, R.A. / Martin-Garcia, J.M. / Ros, A.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_assembly.details / _pdbx_validate_planes.type

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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)37,4626
Polymers35,6732
Non-polymers1,7894
Water2,270126
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,77436
Polymers214,04012
Non-polymers10,73424
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 area62000 Å2
ΔGint-576 kcal/mol
Surface area69320 Å2
MethodPISA
2
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4626
Polymers35,6732
Non-polymers1,7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6700 Å2
ΔGint-82 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.300, 188.300, 61.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-phycocyanin beta chain
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Gene: cpcA, tlr1958 / Production host: Thermosynechococcus vestitus (bacteria) / References: UniProt: P50032
#2: Protein C-phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Gene: cpcB, tlr1957 / Production host: Thermosynechococcus vestitus (bacteria) / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 277 K / Method: batch mode / Details: 75 mM HEPES pH 7.0, 20 mM MgCl2, 9% PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.285 Å
DetectorType: SLAC ePix10k / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.285 Å / Relative weight: 1
ReflectionResolution: 2→24.6 Å / Num. obs: 54596 / % possible obs: 100 % / Redundancy: 28 % / CC1/2: 0.717 / CC star: 0.914 / Net I/σ(I): 1.8
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5458 / CC1/2: 0.144 / CC star: 0.5013
Serial crystallography measurementPulse duration: 40 fsec. / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: Segmnteted Flow / Method: injection
Serial crystallography data reductionCrystal hits: 7465 / Frame hits: 8172 / Frames indexed: 5216 / Frames total: 625979 / Lattices indexed: 7465

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
CrystFEL0.10.1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.31 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.839 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24512 1380 4.9 %RANDOM
Rwork0.2043 ---
obs0.20632 26538 99.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å2-0 Å2
2--0.65 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2→22.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 130 126 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0162683
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162443
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.8113655
X-RAY DIFFRACTIONr_angle_other_deg0.4531.5565658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365.242351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.413520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11710409
X-RAY DIFFRACTIONr_chiral_restr0.0520.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_mcbond_it1.3091.3711339
X-RAY DIFFRACTIONr_mcbond_other1.3041.3711339
X-RAY DIFFRACTIONr_mcangle_it1.9342.0471672
X-RAY DIFFRACTIONr_mcangle_other1.9352.0491673
X-RAY DIFFRACTIONr_scbond_it2.4561.7761344
X-RAY DIFFRACTIONr_scbond_other2.4551.7751343
X-RAY DIFFRACTIONr_scangle_other3.7692.5521984
X-RAY DIFFRACTIONr_long_range_B_refined5.44519.5453011
X-RAY DIFFRACTIONr_long_range_B_other5.42518.942994
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 107 -
Rwork0.362 1914 -
obs--99.7 %
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)
11.45630.5377-0.07630.9485-0.1680.55110.01950.01260.00930.0346-0.00280.01110.01670.0181-0.01660.01940.0028-0.00860.0020.01330.21751.99538.049-6.53
22.0560.23790.15070.28970.19350.14380.0569-0.3014-0.07050.0779-0.05150.06330.0354-0.0154-0.00530.0826-0.01720.02120.12450.00270.2711-3.83529.37918.159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 162
2X-RAY DIFFRACTION2B1 - 172

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