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- PDB-5uvk: Serial Millisecond Crystallography of Membrane and Soluble Protei... -

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Basic information

Entry
Database: PDB / ID: 5uvk
TitleSerial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsELECTRON TRANSPORT / Multi-protein cofactor antenna complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMartin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. ...Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketawala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
Funding support United States, 8items
OrganizationGrant numberCountry
Flinn Foundation1991 United States
STC Program of the National Science Foundation through BioXFEL1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM094618 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Y1-CO-1020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
Department of Energy (DOE, United States)DE-AC02-06CH1135 United States
CitationJournal: Iucrj / Year: 2017
Title: Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.
Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / ...Authors: Martin-Garcia, J.M. / Conrad, C.E. / Nelson, G. / Stander, N. / Zatsepin, N.A. / Zook, J. / Zhu, L. / Geiger, J. / Chun, E. / Kissick, D. / Hilgart, M.C. / Ogata, C. / Ishchenko, A. / Nagaratnam, N. / Roy-Chowdhury, S. / Coe, J. / Subramanian, G. / Schaffer, A. / James, D. / Ketwala, G. / Venugopalan, N. / Xu, S. / Corcoran, S. / Ferguson, D. / Weierstall, U. / Spence, J.C.H. / Cherezov, V. / Fromme, P. / Fischetti, R.F. / Liu, W.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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
Water00
1
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
Water0
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 area60480 Å2
ΔGint-507 kcal/mol
Surface area66690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.400, 186.400, 60.300
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
Source: (gene. exp.) Thermosynechococcus elongatus (strain 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 elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: cpcB, tlr1957 / Production host: Thermosynechococcus elongatus (bacteria) / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7 / Details: 75 mM HEPES pH 7, 20 mM MgCl2, 9 % PEG 3350

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→50.01 Å / Num. obs: 6280 / % possible obs: 99.7 % / Redundancy: 156.4 % / CC1/2: 0.986 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.18 Å / CC1/2: 0.799

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
CrystFEL0.6.2data scaling
CrystFEL0.6.2data reduction
MOLREPphasing
Cheetahdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZIZ

4ziz


Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.652 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20474 1082 14.7 %RANDOM
Rwork0.17248 ---
obs0.17723 6280 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.35 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 129 0 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022671
X-RAY DIFFRACTIONr_bond_other_d0.0030.022535
X-RAY DIFFRACTIONr_angle_refined_deg2.0932.0183636
X-RAY DIFFRACTIONr_angle_other_deg1.05835790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0125332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34524.404109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37515407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1881517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023102
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3624.6391334
X-RAY DIFFRACTIONr_mcbond_other2.3624.6381333
X-RAY DIFFRACTIONr_mcangle_it3.7656.9621664
X-RAY DIFFRACTIONr_mcangle_other3.7646.9631665
X-RAY DIFFRACTIONr_scbond_it3.0944.9561333
X-RAY DIFFRACTIONr_scbond_other3.0934.9561334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0567.3061972
X-RAY DIFFRACTIONr_long_range_B_refined7.71144.58911384
X-RAY DIFFRACTIONr_long_range_B_other7.71144.58911385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 85 -
Rwork0.321 466 -
obs--99.82 %

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