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- PDB-7r30: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

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Basic information

Entry
Database: PDB / ID: 7r30
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with ADP and AMP resulting from ADP soak
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / 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 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BICARBONATE ION / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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
Revision 1.3Nov 6, 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

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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)41,2918
Polymers39,6663
Non-polymers1,6255
Water1,31573
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)63.637, 63.637, 82.207
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
12CYSCYSAA2 - 1102 - 110
22CYSCYSCC2 - 1102 - 110
13SERSERBB2 - 1142 - 114
23SERSERCC2 - 1142 - 114

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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M SODIUM ACETATE, 0.1 M HEPES PH 7.5, 20 % (W/V) PEG3000

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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: 1.9→32.95 Å / Num. obs: 29447 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.5
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.537 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 4769 / CC1/2: 0.713 / % possible all: 100

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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: 5O3P

5o3p


Resolution: 1.9→32.95 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 7.03 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 1467 5 %RANDOM
Rwork0.1709 ---
obs0.1721 27980 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.03 Å2 / Biso mean: 50.994 Å2 / Biso min: 29.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å2-0 Å2
2--0.52 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 1.9→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 96 73 2465
Biso mean--48.72 53.2 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192461
X-RAY DIFFRACTIONr_bond_other_d0.0080.022373
X-RAY DIFFRACTIONr_angle_refined_deg2.0742.0133324
X-RAY DIFFRACTIONr_angle_other_deg1.41935492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79825.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97415434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.811157
X-RAY DIFFRACTIONr_chiral_restr0.1220.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02498
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54200.11
12B54200.11
21A54680.1
22C54680.1
31B54480.13
32C54480.13
LS refinement shellResolution: 1.9→1.948 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.342 95 -
Rwork0.361 2079 -
obs--99.95 %
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)
13.07560.9251-0.42665.02760.06792.46480.01850.0410.1342-0.1258-0.02390.4925-0.2125-0.33840.00540.06990.0869-0.03350.1558-0.02940.0648-14.9522.8017-1.8176
23.8365-1.0801-0.34094.0176-0.19122.7060.105-0.2418-0.00370.2363-0.04330.2135-0.0411-0.1032-0.06160.063-0.0247-0.00190.09790.00160.0202-6.46377.72638.0027
31.16020.1115-0.01243.3305-1.85834.8758-0.0082-0.0770.0054-0.0514-0.0468-0.2182-0.13850.19790.0550.0531-0.01030.01690.0708-0.01150.02774.501818.4269-4.9835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION2B2 - 114
3X-RAY DIFFRACTION3C2 - 114

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