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- PDB-4z8k: Phycocyanin structure from T. elongatus at 2.5-A from XFEL using ... -

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Basic information

Entry
Database: PDB / ID: 4z8k
TitlePhycocyanin structure from T. elongatus at 2.5-A from XFEL using a viscous delivery medium for serial femtosecond crystallography
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Phycocyanin / T.elongatus / Phycobiliprotein / SFX / XFEL / Agarose / Viscous delivery medium.
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: 2.5 Å
AuthorsFromme, R. / Basu, S. / Fromme, P.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094599 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM108635 United States
Department of Energy (DOE, United States)DE-SC001057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097463 United States
CitationJournal: Iucrj / Year: 2015
Title: A novel inert crystal delivery medium for serial femtosecond crystallography.
Authors: Conrad, C.E. / Basu, S. / James, D. / Wang, D. / Schaffer, A. / Roy-Chowdhury, S. / Zatsepin, N.A. / Aquila, A. / Coe, J. / Gati, C. / Hunter, M.S. / Koglin, J.E. / Kupitz, C. / Nelson, G. / ...Authors: Conrad, C.E. / Basu, S. / James, D. / Wang, D. / Schaffer, A. / Roy-Chowdhury, S. / Zatsepin, N.A. / Aquila, A. / Coe, J. / Gati, C. / Hunter, M.S. / Koglin, J.E. / Kupitz, C. / Nelson, G. / Subramanian, G. / White, T.A. / Zhao, Y. / Zook, J. / Boutet, S. / Cherezov, V. / Spence, J.C. / Fromme, R. / Weierstall, U. / Fromme, P.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 19, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,4535
Polymers35,6872
Non-polymers1,7663
Water1,76598
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,36015
Polymers107,0626
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area24440 Å2
ΔGint-240 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.400, 153.400, 39.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17470.656 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.: 98 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.4
Details: 1.0 M ammonium sulfate, 40 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH= 6.4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.33 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 2, 2014
RadiationMonochromator: KB mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.5→29.5 Å / Num. obs: 18908 / % possible obs: 100 % / Redundancy: 250.67 % / Net I/σ(I): 3.19
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1894refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GY3

4gy3


Resolution: 2.5→29.5 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 945 5.01 %Random selection
Rwork0.1871 ---
obs0.1905 18871 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 129 98 2725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162675
X-RAY DIFFRACTIONf_angle_d1.7863637
X-RAY DIFFRACTIONf_dihedral_angle_d17.335955
X-RAY DIFFRACTIONf_chiral_restr0.061402
X-RAY DIFFRACTIONf_plane_restr0.007470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.35531390.32772528X-RAY DIFFRACTION100
2.6318-2.79650.35741390.27992522X-RAY DIFFRACTION100
2.7965-3.01230.33681160.24062542X-RAY DIFFRACTION100
3.0123-3.3150.29051510.20822537X-RAY DIFFRACTION100
3.315-3.79390.23571300.15862553X-RAY DIFFRACTION100
3.7939-4.77660.18741270.13022580X-RAY DIFFRACTION100
4.7766-29.53730.19761430.14262664X-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)
10.06960.0594-0.07010.0747-0.02370.10030.0536-0.07490.05520.0943-0.10620.1128-0.0051-0.06050.00010.2819-0.06830.0140.369-0.00780.277943.5658-50.12167.8981
20.07740.08090.10110.25310.10110.13620.1114-0.25380.33160.1564-0.05370.2872-0.1456-0.13480.01260.39150.07530.05180.35-0.08370.500639.8565-24.21475.83
30.0193-0.0139-0.00490.02470.00410.00380.0397-0.048-0.0091-0.08870.0178-0.0370.03060.03230.00070.2895-0.0167-0.01470.35770.03970.383345.4441-42.4107-3.7578
40.0259-0.0536-0.06380.43380.01670.23310.0055-0.10590.19170.0737-0.12250.12540.07370.0162-0.29240.1657-0.1226-0.04040.28330.00410.257638.7619-53.8615-0.4404
50.32610.01080.05590.1322-0.04580.01770.03510.1486-0.0980.0593-0.0476-0.0786-0.01240.00570.10360.1761-0.06830.00450.30690.00660.184458.2067-65.8009-5.0135
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 174 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 15 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 174 )

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