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- PDB-7r32: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 7r32
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803, delta104 variant, in complex with ADP (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'-DIPHOSPHATE / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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)39,3086
Polymers38,0263
Non-polymers1,2823
Water2,054114
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)73.980, 73.980, 88.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
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 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 2 - 102 / Label seq-ID: 2 - 102

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Membrane-associated protein slr1513


Mass: 12675.491 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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: Molecular Dimensions Morpheus screen condition B9

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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: 1.75→56.74 Å / Num. obs: 47404 / % possible obs: 98.8 % / Redundancy: 9.89 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.422 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 7186 / CC1/2: 0.742 / % possible all: 97.7

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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: 1.75→56.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.023 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2376 5 %RANDOM
Rwork0.1864 ---
obs0.1876 45028 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 33.193 Å2 / Biso min: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å20 Å2
2--0.47 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.75→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 81 114 2303
Biso mean--28.98 41.31 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192224
X-RAY DIFFRACTIONr_bond_other_d0.0090.022178
X-RAY DIFFRACTIONr_angle_refined_deg2.4012.0183004
X-RAY DIFFRACTIONr_angle_other_deg1.59535006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01524.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56615406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9371511
X-RAY DIFFRACTIONr_chiral_restr0.1470.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022390
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02460
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50070.12
12B50070.12
21A51510.1
22C51510.1
31B50500.12
32C50500.12
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 163 -
Rwork0.358 3291 -
all-3454 -
obs--97.65 %
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)
13.50930.2926-0.53964.0106-0.26123.75170.06590.1343-0.0075-0.1627-0.0049-0.1228-0.0627-0.1216-0.0610.00980.00440.00660.048-0.00580.0069-5.918629.8037-11.8103
22.5272-0.1832-0.56643.59340.86584.72240.061-0.07030.01070.1069-0.0029-0.112-0.09570.0569-0.05810.0248-0.0008-0.00860.0119-0.00820.0113-6.406138.01537.6584
33.1151.00650.46613.93691.18922.01630.0855-0.0608-0.16630.1688-0.0631-0.04370.1477-0.0154-0.02240.0372-0.0366-0.0060.04930.00820.0234-14.620719.24413.3171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 102
2X-RAY DIFFRACTION2B2 - 102
3X-RAY DIFFRACTION3C2 - 102

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