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- PDB-7r31: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 7r31
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803, C105A+C110A variant, in complex with ATP (co-crystal), tetragonal crystal form
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / 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 / ADENOSINE-5'-TRIPHOSPHATE / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 / pdbx_initial_refinement_model

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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)41,33811
Polymers39,4743
Non-polymers1,8648
Water4,252236
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)73.190, 73.190, 89.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Membrane-associated protein slr1513


Mass: 13157.979 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954

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Non-polymers , 5 types, 244 molecules

#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.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES PH 6.5, 25 % (W/V) PEG1000

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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: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→33.85 Å / Num. obs: 71568 / % possible obs: 98.8 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.4
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 8.11 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 11257 / CC1/2: 0.932 / % possible all: 96.8

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Processing

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

5o3p


Resolution: 1.52→33.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.22 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 3533 5 %RANDOM
Rwork0.188 ---
obs0.1889 67097 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.14 Å2 / Biso mean: 28.089 Å2 / Biso min: 14.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0 Å2-0 Å2
2--1.14 Å2-0 Å2
3----2.29 Å2
Refinement stepCycle: final / Resolution: 1.52→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 111 236 2667
Biso mean--23.98 38.91 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192520
X-RAY DIFFRACTIONr_bond_other_d0.0010.022421
X-RAY DIFFRACTIONr_angle_refined_deg2.4192.0213416
X-RAY DIFFRACTIONr_angle_other_deg0.9635584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3745312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53524.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37215447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3281513
X-RAY DIFFRACTIONr_chiral_restr0.1480.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 223 -
Rwork0.391 4221 -
all-4444 -
obs--83.93 %
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)
11.5740.3869-0.39643.19740.45462.15580.03380.1204-0.0829-0.0687-0.07190.1036-0.0722-0.13310.03810.0080.01550.00530.03410.0040.0596-6.087632.3673-11.3805
21.45030.0636-0.76371.74760.02183.8445-0.01090.03950.00430.0357-0.0166-0.0237-0.06480.00290.02750.01410.0007-0.00360.0046-0.01210.055-7.850437.11358.3283
31.53041.13021.16142.68651.91392.94870.0702-0.0026-0.12260.1573-0.0015-0.10320.0904-0.035-0.06870.0168-0.01-0.00720.0157-0.00110.103-13.650619.97875.4631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 203
2X-RAY DIFFRACTION2B3 - 202
3X-RAY DIFFRACTION3C3 - 203

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