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- PDB-6mm2: Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 b... -

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Basic information

Entry
Database: PDB / ID: 6mm2
TitleCarbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to ATP and calcium
ComponentsCarbon regulatory PII-like protein SbtB
KeywordsSIGNALING PROTEIN / PII-like protein / SbtB / regulatory protein
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / metal ion binding
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
ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsKaczmarski, J.A. / Jackson, C.
CitationJournal: Biorxiv / Year: 2019
Title: Structure and function of SbtB from Cyanobium sp. 7001
Authors: Jackson, C. / Kaczmarski, J.A. / Price, D.
History
DepositionSep 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0674
Polymers11,4841
Non-polymers5833
Water2,000111
1
A: Carbon regulatory PII-like protein SbtB
hetero molecules

A: Carbon regulatory PII-like protein SbtB
hetero molecules

A: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20012
Polymers34,4523
Non-polymers1,7489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8300 Å2
ΔGint-152 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.058, 52.058, 95.214
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-384-

HOH

31A-390-

HOH

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Components

#1: Protein Carbon regulatory PII-like protein SbtB


Mass: 11484.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobium sp. PCC 7001 (bacteria) / Gene: CPCC7001_1671 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5II98
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30 % 2-methyl-2,4-pentanediol 0.02 M calcium chloride 0.1 M sodium acetate-acetic acid pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.04→16.045 Å / Num. obs: 44144 / % possible obs: 95.3 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.043 / Χ2: 0.87 / Net I/av σ(I): 21.8 / Net I/σ(I): 0.999
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.337 / Num. unique obs: 2573 / CC1/2: 0.405 / % possible all: 50.9

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Processing

Software
NameVersionClassification
REFMAC1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O3P

5o3p


Resolution: 1.04→16.04 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1632 --
Rwork0.1452 --
obs-44104 95.16 %
Refinement stepCycle: LAST / Resolution: 1.04→16.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms763 0 33 119 915
LS refinement shellResolution: 1.04→1.076 Å
RfactorNum. reflection% reflection
Rfree0.4062 --
Rwork0.3543 --
obs-3026 65.12 %

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