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- PDB-6n4a: PII-like SbtB from Cyanobium sp PCC 7001 (apo) -

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Basic information

Entry
Database: PDB / ID: 6n4a
TitlePII-like SbtB from Cyanobium sp PCC 7001 (apo)
ComponentsPII-like SbtB
KeywordsSIGNALING PROTEIN / Pii-like signalling protein / SbtB / cyanobacteria
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
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
PHOSPHATE ION / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKaczmarski, J.A. / Jackson, C.J.
CitationJournal: Biorxiv / Year: 2019
Title: Structure and function of SbtB from Cyanobium sp. 7001
Authors: Jackson, C. / Kaczmarski, J.A. / Price, D.
History
DepositionNov 18, 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

Downloads & links

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Assembly

Deposited unit
A: PII-like SbtB
B: PII-like SbtB
C: PII-like SbtB
D: PII-like SbtB
E: PII-like SbtB
F: PII-like SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5728
Polymers68,3826
Non-polymers1902
Water39622
1
A: PII-like SbtB
B: PII-like SbtB
C: PII-like SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2864
Polymers34,1913
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-24 kcal/mol
Surface area11590 Å2
MethodPISA
2
D: PII-like SbtB
E: PII-like SbtB
F: PII-like SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2864
Polymers34,1913
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-23 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.622, 51.030, 66.598
Angle α, β, γ (deg.)94.390, 106.130, 103.550
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PII-like SbtB


Mass: 11396.966 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) / References: UniProt: B5II98
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 25 mM Na2H/KH2PO4 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953657 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953657 Å / Relative weight: 1
ReflectionResolution: 2.3→49.03 Å / Num. obs: 24704 / % possible obs: 98 % / Redundancy: 3.8 % / Net I/σ(I): 15.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Num. unique obs: 2386 / CC1/2: 0.574 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.03 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs24695 98.0278 %
Displacement parametersBiso max: 141.6 Å2 / Biso mean: 75.1516 Å2 / Biso min: 32.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 10 22 4004

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