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- PDB-6wue: Tetragonal crystal form of SbtB from Synechocystis PCC6803 -

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Basic information

Entry
Database: PDB / ID: 6wue
TitleTetragonal crystal form of SbtB from Synechocystis PCC6803
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / Regulator of cyanobacterial bicarbonate transporter
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 / ISOPROPYL ALCOHOL / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBu, G. / Simmons, C.R. / Nielsen, D.R. / Nannenga, B.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Tetragonal crystal form of the cyanobacterial bicarbonate-transporter regulator SbtB from Synechocystis sp. PCC 6803.
Authors: Bu, G. / Simmons, C.R. / Nielsen, D.R. / Nannenga, B.L.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: 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 1.3Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1875
Polymers24,0442
Non-polymers1433
Water2,972165
1
A: Membrane-associated protein slr1513
B: Membrane-associated protein slr1513
hetero molecules

A: Membrane-associated protein slr1513
B: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37410
Polymers48,0874
Non-polymers2866
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8240 Å2
ΔGint-43 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.571, 51.571, 178.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Membrane-associated protein slr1513 / Bicarbonate transport regulator SbtB-6803


Mass: 12021.810 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr1513 / Production host: Escherichia coli BW25113 (bacteria) / References: UniProt: P73954
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trisodium citrate, 0.1 M HEPES pH 7.2, 12% (v/v) isopropanol, 0.2 M nickel chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20957 / % possible obs: 89.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 20.12 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.093 / Net I/σ(I): 29.1
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1851 / CC1/2: 0.92 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dfe

3dfe


Resolution: 1.8→33.75 Å / SU ML: 0.1964 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3848 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.205 2000 9.55 %
Rwork0.1864 18948 -
obs0.1882 20948 89.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 9 165 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01941421
X-RAY DIFFRACTIONf_angle_d1.6551920
X-RAY DIFFRACTIONf_chiral_restr0.1329228
X-RAY DIFFRACTIONf_plane_restr0.0089236
X-RAY DIFFRACTIONf_dihedral_angle_d22.156531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.28641470.24811388X-RAY DIFFRACTION92.75
1.84-1.890.24061470.23061401X-RAY DIFFRACTION95.97
1.89-1.950.3634800.3038754X-RAY DIFFRACTION51.29
1.95-2.010.20831520.18591437X-RAY DIFFRACTION97.13
2.01-2.080.19961540.18211458X-RAY DIFFRACTION97.4
2.08-2.170.18961540.17311462X-RAY DIFFRACTION98.42
2.17-2.260.24951070.21621012X-RAY DIFFRACTION68.19
2.26-2.380.21241220.17431165X-RAY DIFFRACTION78.48
2.38-2.530.20671590.16761501X-RAY DIFFRACTION99.82
2.53-2.730.22711610.17541523X-RAY DIFFRACTION99.94
2.73-30.21691610.181517X-RAY DIFFRACTION99.76
3-3.440.19051630.18231551X-RAY DIFFRACTION99.88
3.44-4.330.16061170.1641104X-RAY DIFFRACTION70.7
4.33-33.750.18781760.19231675X-RAY DIFFRACTION99.46

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