PDB-6xwk: Crystal structure of Phormidium rubidum phycocyanin

ID or keywords:

Entry

Database: PDB / ID: 6xwk

Title

Crystal structure of Phormidium rubidum phycocyanin

Components

Phycocyanin alpha subunit
Phycocyanin beta subunit

Keywords

PHOTOSYNTHESIS / Phycocyanin / Phycocyanobilin / Light harvesting / Cyanobacteria

Function / homology

PHYCOCYANOBILIN / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Phormidium rubidum A09DM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.17 Å

Authors

Sonani, R.R. / Roszak, A.W. / Cogdell, R.J. / Madamwar, D. / Liu, H. / Gross, M.L. / Blankenship, R.E.

Funding support

United States, 1items

Citation

Journal: Photosyn. Res. / Year: 2020
Title: Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin.
Authors: Sonani, R.R. / Roszak, A.W. / Liu, H. / Gross, M.L. / Blankenship, R.E. / Madamwar, D. / Cogdell, R.J.

History

Deposition	Jan 23, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6xwk.cif.gz	164.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6xwk_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	6xwk_full_validation.pdf.gz	1.3 MB	Display
Data in XML	6xwk_validation.xml.gz	22 KB	Display
Data in CIF	6xwk_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xw/6xwk ftp://data.pdbj.org/pub/pdb/validation_reports/xw/6xwk	HTTPS FTP

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Related structure data

Related structure data	4yjjS S: Starting model for refinement
Similar structure data	5ook-1 4f0t-1 6yqg-1 4z8k-1 1on7-2 2c7j-1 2c7l-1 4gy3-1 4yjj-1 6hrn-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

AAA: Phycocyanin alpha subunit

BBB: Phycocyanin beta subunit

hetero molecules

38.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Phycocyanin alpha subunit

BBB: Phycocyanin beta subunit

hetero molecules

AAA: Phycocyanin alpha subunit

BBB: Phycocyanin beta subunit

hetero molecules

AAA: Phycocyanin alpha subunit

BBB: Phycocyanin beta subunit

hetero molecules

defined by author&software
Evidence: gel filtration
114 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.320, 106.320, 58.670
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

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Protein , 2 types, 2 molecules AAABBB

#1: Protein	Phycocyanin alpha subunit Mass: 17320.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phormidium rubidum A09DM (bacteria)
#2: Protein	Phycocyanin beta subunit Mass: 18154.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phormidium rubidum A09DM (bacteria)

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Non-polymers , 6 types, 474 molecules

#3: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.42 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: MPD, PEG1000, PEG3350, Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8492 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8492 Å / Relative weight: 1
Reflection	Resolution: 1.17→39.39 Å / Num. obs: 127070 / % possible obs: 100 % / Redundancy: 14 % / CC_1/2: 1 / Net I/σ(I): 21.3
Reflection shell	Resolution: 1.17→1.2 Å / Num. unique obs: 127070 / CC_1/2: 0.51

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4yjj

4yjj

Resolution: 1.17→39.39 Å / Cor.coef. F_o:F_c: 0.986 / Cor.coef. F_o:F_c free: 0.979 / SU B: 1.488 / SU ML: 0.027 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.145	6165	4.853 %
R_work	0.1188	-	-
all	0.12	-	-
obs	-	127046	99.973 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 15.305 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.981 Å²	-0.491 Å²	0 Å²
2-	-	-0.981 Å²	0 Å²
3-	-	-	3.184 Å²

Refinement step

Cycle: LAST / Resolution: 1.17→39.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2484	0	190	463	3137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2975
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	2752
X-RAY DIFFRACTION	r_angle_refined_deg	1.747	1.649	4055
X-RAY DIFFRACTION	r_angle_other_deg	1.71	1.584	6385
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.83	5	399
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.319	20.764	157
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.875	15	471
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	33.699	15	3
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.377	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	385
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3609
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	638
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	731
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	2622
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1473
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1157
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	311
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.131	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.307	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.279	0.2	82
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	56
X-RAY DIFFRACTION	r_mcbond_it	1.58	1.304	1458
X-RAY DIFFRACTION	r_mcbond_other	1.56	1.303	1456
X-RAY DIFFRACTION	r_mcangle_it	1.853	1.965	1854
X-RAY DIFFRACTION	r_mcangle_other	1.833	1.965	1854
X-RAY DIFFRACTION	r_scbond_it	2.454	1.633	1517
X-RAY DIFFRACTION	r_scbond_other	2.453	1.635	1518
X-RAY DIFFRACTION	r_scangle_it	3.126	2.33	2183
X-RAY DIFFRACTION	r_scangle_other	3.127	2.332	2184
X-RAY DIFFRACTION	r_lrange_it	3.81	18.383	3645
X-RAY DIFFRACTION	r_lrange_other	3.15	17.173	3502
X-RAY DIFFRACTION	r_rigid_bond_restr	4.404	3	5727

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.17-1.2	0.284	449	0.272	8926	X-RAY DIFFRACTION	99.968
1.2-1.233	0.259	408	0.251	8710	X-RAY DIFFRACTION	100
1.233-1.269	0.22	471	0.22	8401	X-RAY DIFFRACTION	99.9887
1.269-1.308	0.208	413	0.205	8214	X-RAY DIFFRACTION	100
1.308-1.351	0.187	471	0.172	7872	X-RAY DIFFRACTION	100
1.351-1.398	0.177	389	0.156	7703	X-RAY DIFFRACTION	100
1.398-1.451	0.156	377	0.137	7415	X-RAY DIFFRACTION	99.9872
1.451-1.51	0.153	382	0.111	7133	X-RAY DIFFRACTION	99.9468
1.51-1.577	0.121	314	0.09	6881	X-RAY DIFFRACTION	99.9722
1.577-1.654	0.122	332	0.083	6554	X-RAY DIFFRACTION	99.9855
1.654-1.744	0.121	257	0.08	6329	X-RAY DIFFRACTION	99.9848
1.744-1.849	0.108	302	0.077	5871	X-RAY DIFFRACTION	99.9676
1.849-1.977	0.128	303	0.092	5564	X-RAY DIFFRACTION	99.983
1.977-2.135	0.125	257	0.097	5181	X-RAY DIFFRACTION	99.9816
2.135-2.338	0.119	277	0.087	4743	X-RAY DIFFRACTION	99.9403
2.338-2.613	0.116	210	0.089	4321	X-RAY DIFFRACTION	100
2.613-3.016	0.114	172	0.098	3852	X-RAY DIFFRACTION	99.9007
3.016-3.691	0.15	175	0.121	3254	X-RAY DIFFRACTION	99.9417
3.691-5.205	0.141	121	0.12	2529	X-RAY DIFFRACTION	100
5.205-39.39	0.188	85	0.172	1429	X-RAY DIFFRACTION	99.6053

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