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- PDB-4q70: Light Harvesting Protein Phycocyanin in high resolution using a f... -

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Basic information

Entry
Database: PDB / ID: 4q70
TitleLight Harvesting Protein Phycocyanin in high resolution using a femtosecond X-Ray laser
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Femtosecond Crystallography Phycocyanin Photosynthesis / Phycobilisome
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 / molecular replacement / Resolution: 1.85 Å
AuthorsFromme, R. / Roy-Chowdhury, S. / Basu, S. / Yoon, C. / Fromme, P.
CitationJournal: TO BE PUBLISHED
Title: Observations on the Light Harvesting Protein Phycocyanin structure in high resolution using a femtosecond X-Ray laser
Authors: Fromme, R. / Roy-Chowdhury, S. / Basu, S. / Yoon, C. / Brune, D. / Fromme, P.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water3,405189
1
B: C-phycocyanin beta chain
hetero molecules

B: C-phycocyanin beta chain
hetero molecules

B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,31815
Polymers107,0206
Non-polymers5,2989
Water1086
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_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area25050 Å2
ΔGint-242 kcal/mol
Surface area42720 Å2
MethodPISA
2
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_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area61460 Å2
ΔGint-514 kcal/mol
Surface area74080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.800, 192.800, 62.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21B-303-

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 (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 (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.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 14187

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 277 K / Method: batch / pH: 7
Details: 10-18 % PEG 3350, 10-100 mM NaCl, 0-100 mM MgCl2, pH 7.0, Batch, temperature 277K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.34 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Jan 25, 2014
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.85→36.436 Å / Num. all: 37798 / Num. obs: 37798 / % possible obs: 100 % / Observed criterion σ(I): 1.37

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.9_1675refinement
PDB_EXTRACT3.14data extraction
Cheetahdata collection
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.436 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 1952 5.16 %
Rwork0.2042 --
obs0.2079 37798 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.71 Å2 / Biso mean: 29.0429 Å2 / Biso min: 3.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 129 189 2815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152674
X-RAY DIFFRACTIONf_angle_d1.4253636
X-RAY DIFFRACTIONf_chiral_restr0.056402
X-RAY DIFFRACTIONf_plane_restr0.005470
X-RAY DIFFRACTIONf_dihedral_angle_d17.703954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.89630.42371300.355225442674
1.8963-1.94760.41191430.345225562699
1.9476-2.00490.41441470.333625242671
2.0049-2.06960.39061470.316425462693
2.0696-2.14350.37261090.294425652674
2.1435-2.22940.33391360.265625452681
2.2294-2.33080.32331350.255525662701
2.3308-2.45370.32761320.240125512683
2.4537-2.60730.33131460.224325552701
2.6073-2.80860.2631400.205125532693
2.8086-3.09110.26791460.182525532699
3.0911-3.53810.23031390.152925852724
3.5381-4.45630.17171500.125325682718
4.4563-36.44280.20271520.129126352787
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)
10.07110.1169-0.16980.1858-0.27920.415-0.0992-0.08940.10750.0559-0.1235-0.1182-0.14380.0453-0.05990.1230.035-0.02530.1503-0.05890.2243-10.5386-24.2158-36.8612
20.24630.019-0.02050.1064-0.10.0443-0.0308-0.1352-0.1173-0.01910.04890.0946-0.00980.01150.00010.1496-0.0015-0.02340.207-0.02260.26-37.1464-23.7783-38.0924
30.4230.1237-0.04250.35430.17250.4626-0.0138-0.0266-0.1399-0.00970.0070.1726-0.07630.0212-0.00090.15810.0022-0.00590.16420.00840.1857-38.653-13.0251-38.0635
40.38620.0647-0.20740.0163-0.0220.12440.1327-0.15150.08720.07120.00440.1191-0.25580.0370.26910.15950.02370.08820.17580.11260.0288-5.8404-34.5988-12.4284
50.0808-0.2092-0.09450.77040.1770.0506-0.08130.0328-0.16680.1059-0.11050.1923-0.03520.0661-0.21790.14780.01610.02890.20950.02130.1666-28.8643-18.0216-14.2724
60.11-0.1670.01910.239-0.02360.1417-0.0879-0.07160.03210.09990.1737-0.1256-0.05420.06530.11430.10390.0564-0.09410.2468-0.03250.0928-24.2225-9.5555-17.2182
70.0957-0.198-0.10.53670.17210.3196-0.0359-0.1550.06230.20470.2294-0.2289-0.1438-0.05330.66160.16670.0368-0.10330.21190.00010.1307-22.3184-11.9478-9.0327
80.5334-0.304-0.19570.5926-0.24030.529-0.2368-0.0078-0.03770.23940.0294-0.05650.0613-0.0051-0.55410.14320.08410.0090.21530.00160.0843-29.5917-25.7679-10.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 67 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 162 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 20 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 75 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 99 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 142 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 143 through 172 )B0

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