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

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Basic information

Entry
Database: PDB / ID: 7obj
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with cyclic di-AMP (c-di-AMP)
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / SbtB / Carbon Sensing / PII-like / Cyanobacteria
Function / homologyNitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / regulation of nitrogen utilization / plasma membrane-derived thylakoid membrane / enzyme regulator activity / Chem-2BA / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSelim, K.A. / Albrecht, R. / Hartmann, M.D.
CitationJournal: Sci Adv / Year: 2021
Title: Diurnal metabolic control in cyanobacteria requires perception of second messenger signaling molecule c-di-AMP by the carbon control protein SbtB.
Authors: Selim, K.A. / Haffner, M. / Burkhardt, M. / Mantovani, O. / Neumann, N. / Albrecht, R. / Seifert, R. / Kruger, L. / Stulke, J. / Hartmann, M.D. / Hagemann, M. / Forchhammer, K.
History
DepositionApr 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)40,9835
Polymers39,6663
Non-polymers1,3172
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-31 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.171, 63.171, 81.733
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
11CYSCYSAA2 - 1102 - 110
21CYSCYSBB2 - 1102 - 110
12SERSERAA2 - 1112 - 111
22SERSERCC2 - 1112 - 111
13SERSERBB2 - 1112 - 111
23SERSERCC2 - 1112 - 111

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-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M phosphate-citrate pH 4.2, 40% (w/v) PEG 300

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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→32.74 Å / Num. obs: 24685 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.61
Reflection shellResolution: 2→2.12 Å / Redundancy: 10.1 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 3942 / CC1/2: 0.43

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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: 5O3R

5o3r


Resolution: 2→32.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 9.758 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1231 5 %RANDOM
Rwork0.1779 ---
obs0.1797 23454 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.69 Å2 / Biso mean: 57.982 Å2 / Biso min: 35.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å2-0 Å2
2--0.41 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 88 105 2480
Biso mean--64 60.67 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192445
X-RAY DIFFRACTIONr_bond_other_d0.0080.022349
X-RAY DIFFRACTIONr_angle_refined_deg1.9272.0223316
X-RAY DIFFRACTIONr_angle_other_deg1.3235437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03725.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63115434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.179156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022641
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02491
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54400.12
12B54400.12
21A54820.11
22C54820.11
31B53460.13
32C53460.13
LS refinement shellResolution: 2→2.049 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.387 84 -
Rwork0.376 1675 -
obs--95.44 %
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)
14.33510.7713-0.68613.7318-0.10533.14270.00440.08210.1193-0.1890.06070.4254-0.1627-0.4036-0.06510.10490.0805-0.0540.12280.01120.0844-14.959122.2039-2.0321
25.1-1.3332-0.31865.0509-0.56272.44930.0809-0.2485-0.05950.11570.04610.133-0.1082-0.1866-0.1270.0891-0.0237-0.03190.0650.02470.0275-6.44877.70697.8577
31.710.687-0.72373.9785-1.65956.11730.0089-0.1074-0.1099-0.02660.0101-0.3157-0.17380.2257-0.0190.0943-0.0276-0.00380.0277-0.02030.07994.441518.1974-5.4375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION2B2 - 114
3X-RAY DIFFRACTION3C2 - 112

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