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- PDB-5o3p: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 5o3p
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in Apo state, trigonal 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
DI(HYDROXYETHYL)ETHER / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSelim, K.A. / Albrecht, R. / Forchhammer, K. / Hartmann, M.D.
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 1.3Nov 6, 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
B: Membrane-associated protein slr1513
C: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2496
Polymers39,6663
Non-polymers5833
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-31 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.351, 64.351, 82.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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 / Plasmid: pASK-IBA3C / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.2
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 0.1 M phosphate-citrate pH 4.2, and 40 % (w/v) PEG300.

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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: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→33.16 Å / Num. obs: 38551 / % possible obs: 99.7 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.62
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6130 / CC1/2: 0.777 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DFE

3dfe


Resolution: 1.75→33.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.409 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19377 1898 4.9 %RANDOM
Rwork0.16374 ---
obs0.16525 36652 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å2-0 Å2
2--0.43 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.75→33.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 39 178 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192388
X-RAY DIFFRACTIONr_bond_other_d0.0010.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9793211
X-RAY DIFFRACTIONr_angle_other_deg0.92235419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96225.39389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.999156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
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_it2.4692.6561215
X-RAY DIFFRACTIONr_mcbond_other2.4552.6541214
X-RAY DIFFRACTIONr_mcangle_it3.2393.9511518
X-RAY DIFFRACTIONr_mcangle_other3.2383.9531519
X-RAY DIFFRACTIONr_scbond_it3.7723.0941173
X-RAY DIFFRACTIONr_scbond_other3.7723.0941173
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3974.4461692
X-RAY DIFFRACTIONr_long_range_B_refined7.83722.9862688
X-RAY DIFFRACTIONr_long_range_B_other7.79422.4422621
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.748→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 125 -
Rwork0.315 2614 -
obs--95.47 %
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)
13.57310.7638-0.89062.9623-0.2042.69780.06160.18210.0711-0.25210.03280.2513-0.1098-0.3138-0.09440.05270.0318-0.02850.05210.00330.0283-14.447722.7818-1.6298
23.3172-1.01830.1013.5033-0.43811.8740.0698-0.2141-0.133-0.01140.02510.13470.0096-0.0909-0.0950.0118-0.0099-0.01310.0210.01610.0217-6.7088.46147.762
31.3352-0.4360.03422.6881-2.34025.11230.0179-0.0016-0.1305-0.066-0.0287-0.1552-0.03190.20130.01070.0089-0.0070.00590.012-0.00630.03825.145418.2996-4.4784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 200
2X-RAY DIFFRACTION2B2 - 201
3X-RAY DIFFRACTION3C2 - 114

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