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

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Basic information

Entry
Database: PDB / ID: 6mmq
TitleCarbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to cAMP
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-3',5'-CYCLIC-MONOPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
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
B: Carbon regulatory PII-like protein SbtB
D: Carbon regulatory PII-like protein SbtB
C: Carbon regulatory PII-like protein SbtB
E: Carbon regulatory PII-like protein SbtB
F: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,88012
Polymers68,9046
Non-polymers1,9756
Water61334
1
A: Carbon regulatory PII-like protein SbtB
B: Carbon regulatory PII-like protein SbtB
D: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4406
Polymers34,4523
Non-polymers9883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-11 kcal/mol
Surface area11440 Å2
MethodPISA
2
C: Carbon regulatory PII-like protein SbtB
E: Carbon regulatory PII-like protein SbtB
F: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4406
Polymers34,4523
Non-polymers9883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-12 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.649, 50.211, 66.561
Angle α, β, γ (deg.)97.60, 102.85, 102.49
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Carbon regulatory PII-like protein SbtB


Mass: 11484.044 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobium sp. PCC 7001 (bacteria) / Gene: CPCC7001_1671 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5II98
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Acetate, 16 % PEG 3350

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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: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→42.48 Å / Num. obs: 35671 / % possible obs: 96.4 % / Redundancy: 2.4 % / Net I/σ(I): 6.4
Reflection shellResolution: 2.02→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→42.472 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1792 5.03 %
Rwork0.2184 --
obs0.2214 35630 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→42.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 132 34 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084193
X-RAY DIFFRACTIONf_angle_d1.0055691
X-RAY DIFFRACTIONf_dihedral_angle_d6.6762943
X-RAY DIFFRACTIONf_chiral_restr0.055687
X-RAY DIFFRACTIONf_plane_restr0.004667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0201-2.07470.47061300.41132574X-RAY DIFFRACTION96
2.0747-2.13580.42011360.3732628X-RAY DIFFRACTION97
2.1358-2.20470.4041340.33562631X-RAY DIFFRACTION97
2.2047-2.28350.37121520.3022598X-RAY DIFFRACTION97
2.2835-2.37490.34391390.27682626X-RAY DIFFRACTION97
2.3749-2.4830.29541270.25592628X-RAY DIFFRACTION97
2.483-2.61390.39041460.25282615X-RAY DIFFRACTION97
2.6139-2.77760.32081260.24752649X-RAY DIFFRACTION97
2.7776-2.9920.35061330.26662605X-RAY DIFFRACTION97
2.992-3.2930.351460.2512571X-RAY DIFFRACTION95
3.293-3.76930.32081220.23772550X-RAY DIFFRACTION94
3.7693-4.74790.24391440.18672553X-RAY DIFFRACTION95
4.7479-42.48140.20971570.17332610X-RAY DIFFRACTION97

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