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- PDB-7s50: Serial Macromolecular Crystallography at ALBA Synchrotron Light S... -

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Basic information

Entry
Database: PDB / ID: 7s50
TitleSerial Macromolecular Crystallography at ALBA Synchrotron Light Source - Phycocyanin
Components(C-phycocyanin ...) x 2
KeywordsELECTRON TRANSPORT / Serial Crystallography / LCP Injection
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMartin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. ...Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, R. / Carpena, X.
Funding support2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306
Other government2019-T1BMD-15552
CitationJournal: J.Synchrotron Radiat. / Year: 2022
Title: Serial macromolecular crystallography at ALBA Synchrotron Light Source.
Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / ...Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, D.R. / Carpena, X.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1Oct 25, 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)37,4987
Polymers35,6732
Non-polymers1,8255
Water77543
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,98742
Polymers214,04012
Non-polymers10,94730
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 area63170 Å2
ΔGint-630 kcal/mol
Surface area69670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.500, 188.500, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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C-phycocyanin ... , 2 types, 2 molecules AB

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / Gene: cpcA, tlr1958 / Production host: Thermosynechococcus elongatus (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)
Strain: BP-1 / Gene: cpcB, tlr1957 / Production host: Thermosynechococcus elongatus (bacteria) / References: UniProt: P50033

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Non-polymers , 4 types, 48 molecules

#3: Chemical ChemComp-CYC / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.07 %
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: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→48.8 Å / Num. obs: 24059 / % possible obs: 100 % / Redundancy: 3023 % / Biso Wilson estimate: 42.3 Å2 / CC1/2: 0.9968 / CC star: 0.9992 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 712 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2370 / CC1/2: 0.0458 / CC star: 0.296 / % possible all: 100
Serial crystallography sample deliveryDescription: LCP Injection / Method: injection
Serial crystallography sample delivery injectionInjector diameter: 5.0E-5 µm
Serial crystallography data reductionFrames total: 753533 / Lattices indexed: 152142

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELv0.10.0data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVK

5uvk


Resolution: 2.1→43.42 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.853 / SU B: 17.535 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.34685 1185 4.9 %RANDOM
Rwork0.30474 ---
obs0.30684 22830 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å2-0 Å2
2---0.25 Å2-0 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 140 43 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0172669
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192535
X-RAY DIFFRACTIONr_angle_refined_deg0.8391.8613630
X-RAY DIFFRACTIONr_angle_other_deg0.9122.6475789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0925330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70920.828145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8351517
X-RAY DIFFRACTIONr_chiral_restr0.0390.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_mcbond_it0.4835.4221332
X-RAY DIFFRACTIONr_mcbond_other0.4835.4221332
X-RAY DIFFRACTIONr_mcangle_it0.838.131658
X-RAY DIFFRACTIONr_mcangle_other0.8298.1311659
X-RAY DIFFRACTIONr_scbond_it0.3495.4671336
X-RAY DIFFRACTIONr_scbond_other0.3495.4661335
X-RAY DIFFRACTIONr_scangle_other0.6048.191973
X-RAY DIFFRACTIONr_long_range_B_refined2.5965.8293021
X-RAY DIFFRACTIONr_long_range_B_other2.43865.8063019
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1453 78 -
Rwork0.1396 1530 -
obs--90.03 %

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