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- PDB-5o3s: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 5o3s
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in Apo state, hexagonal crystal form
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / SbtB / Carbon sensing / PII-like / cyanobacteria
Function / homology
Function and homology information


regulation of nitrogen utilization / plasma membrane-derived thylakoid membrane / enzyme regulator activity
Similarity search - Function
Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSelim, K.A. / Albrecht, R. / Forchhammer, K. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
DAAD/DFG Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: PII-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response.
Authors: Selim, K.A. / Haase, F. / Hartmann, M.D. / Hagemann, M. / Forchhammer, K.
History
DepositionMay 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated protein slr1513


Theoretical massNumber of molelcules
Total (without water)13,2221
Polymers13,2221
Non-polymers00
Water1267
1
A: Membrane-associated protein slr1513

A: Membrane-associated protein slr1513

A: Membrane-associated protein slr1513


Theoretical massNumber of molelcules
Total (without water)39,6663
Polymers39,6663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4910 Å2
ΔGint-29 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.535, 50.535, 64.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

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


Mass: 13222.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.5
Details: Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl mixed 1:1 with reservoir solution composed of 0.2 M Mg chloride, 0.1 M Tris.HCl pH 8.5, and 30% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→36.29 Å / Num. obs: 4838 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.25
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 776 / CC1/2: 0.934 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O3P

5o3p


Resolution: 2.2→36.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 38.876 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26763 581 12 %RANDOM
Rwork0.2261 ---
obs0.23109 4256 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.915 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å2-1.73 Å20 Å2
2---3.45 Å20 Å2
3---11.21 Å2
Refinement stepCycle: 1 / Resolution: 2.2→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 0 7 718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.019721
X-RAY DIFFRACTIONr_bond_other_d0.0010.02697
X-RAY DIFFRACTIONr_angle_refined_deg0.7411.971974
X-RAY DIFFRACTIONr_angle_other_deg0.63531603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.93593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55625.18527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08915124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.514152
X-RAY DIFFRACTIONr_chiral_restr0.0450.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02146
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_it0.4073.931378
X-RAY DIFFRACTIONr_mcbond_other0.4073.93377
X-RAY DIFFRACTIONr_mcangle_it0.7365.893469
X-RAY DIFFRACTIONr_mcangle_other0.7365.894470
X-RAY DIFFRACTIONr_scbond_it0.363.943343
X-RAY DIFFRACTIONr_scbond_other0.363.943343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5995.9506
X-RAY DIFFRACTIONr_long_range_B_refined1.44130.478750
X-RAY DIFFRACTIONr_long_range_B_other1.44130.477750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 42 -
Rwork0.396 303 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: -0.8765 Å / Origin y: 17.3722 Å / Origin z: 0.3151 Å
111213212223313233
T0.1021 Å2-0.0212 Å2-0.0205 Å2-0.0181 Å2-0.0472 Å2--0.2571 Å2
L11.9638 °2-1.2304 °2-1.6324 °2-7.4958 °20.615 °2--4.4445 °2
S-0.0067 Å °0.3421 Å °-1.7283 Å °-0.1014 Å °-0.1702 Å °0.2592 Å °0.4188 Å °-0.1828 Å °0.1768 Å °

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