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- PDB-7r2y: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 7r2y
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with ATP resulting from short ATP soak, conflicting T-loop and C-loop with partial occupancy
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / CARBON SENSING / PII-LIKE / CYANOBACTERIA
Function / homologyNitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / plasma membrane-derived thylakoid membrane / ADENOSINE-5'-TRIPHOSPHATE / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsSelim, K.A. / Albrecht, R. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA.
Authors: Selim, K.A. / Haffner, M. / Mantovani, O. / Albrecht, R. / Zhu, H. / Hagemann, M. / Forchhammer, K. / Hartmann, M.D.
History
DepositionFeb 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: 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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated protein slr1513
B: Membrane-associated protein slr1513
C: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2348
Polymers39,6663
Non-polymers1,5685
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.833, 63.833, 81.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA2 - 1112 - 111
21SERSERBB2 - 1112 - 111
12ALAALAAA2 - 1122 - 112
22ALAALACC2 - 1122 - 112
13TRPTRPBB2 - 1132 - 113
23TRPTRPCC2 - 1132 - 113

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Membrane-associated protein slr1513 / SbtB protein


Mass: 13222.110 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2M SODIUM ACETATE, 0.1M HEPES PH 7.5, 20% (W/V) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→32.73 Å / Num. obs: 20143 / % possible obs: 99.6 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 1.395 / Num. unique obs: 3177 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5O3P

5o3p


Resolution: 2.15→32.73 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 11.7 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 1007 5 %RANDOM
Rwork0.1801 ---
obs0.1817 19135 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.38 Å2 / Biso mean: 70.172 Å2 / Biso min: 41.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å2-0 Å2
2--1.04 Å2-0 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.15→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 95 36 2451
Biso mean--72.98 67.84 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192477
X-RAY DIFFRACTIONr_bond_other_d0.0070.022364
X-RAY DIFFRACTIONr_angle_refined_deg1.9572.0163359
X-RAY DIFFRACTIONr_angle_other_deg1.34335463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7862590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86715438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.556158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022674
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02505
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53530.09
12B53530.09
21A52700.11
22C52700.11
31B53890.12
32C53890.12
LS refinement shellResolution: 2.15→2.202 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.439 70 -
Rwork0.366 1368 -
obs--94.61 %
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)
14.31650.7291-0.30365.61340.6354.31180.0330.14340.1697-0.18870.08750.5147-0.3626-0.4786-0.12060.0990.1097-0.05290.1566-0.0010.1356-14.976522.7431-1.5768
24.4781-0.8852-0.52795.3686-0.23633.44950.0135-0.2833-0.05510.21730.04970.5141-0.1096-0.1846-0.06320.0532-0.011-0.00150.07490.01730.0637-6.70817.81448.084
32.29850.3558-1.24734.7867-1.8336.9185-0.0081-0.09370.0613-0.0468-0.0399-0.254-0.26970.24910.04790.0478-0.026-0.00040.0309-0.02720.07984.404518.6323-5.3659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 112
2X-RAY DIFFRACTION2B2 - 114
3X-RAY DIFFRACTION3C2 - 113

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