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- PDB-6ntb: PII-like SbtB from Cyanobium sp PCC 7001 bound to ATP -

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Basic information

Entry
Database: PDB / ID: 6ntb
TitlePII-like SbtB from Cyanobium sp PCC 7001 bound to ATP
ComponentsSbtB7001, PII-like protein
KeywordsSIGNALING PROTEIN / Pii-like signalling protein / SbtB
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: 1.9 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
DepositionJan 28, 2019Deposition 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

Downloads & links

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Assembly

Deposited unit
A: SbtB7001, PII-like protein
B: SbtB7001, PII-like protein
C: SbtB7001, PII-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0097
Polymers34,4523
Non-polymers1,5574
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-27 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.946, 132.946, 33.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

#1: Protein SbtB7001, PII-like protein


Mass: 11484.044 Da / Num. of mol.: 3
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Lithium Chloride, 20 % PEG 6000, 100 mM sodium acetate-acetic acid, pH 5

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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: 1.9→43.52 Å / Num. obs: 27468 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 36.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.035 / Rrim(I) all: 0.112 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 18.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2714 / CC1/2: 0.56 / Rpim(I) all: 0.925 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MM2

6mm2


Resolution: 1.9→43.52 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.195 --
obs-27454 100 %
Refinement stepCycle: LAST / Resolution: 1.9→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 94 61 2473
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.3882 0 -
Rwork0.316 0 -
obs--100 %
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)
12.93861.3002-1.03022.04591.56943.03050.00840.14880.2609-0.01340.1038-0.2511-0.72860.41050.00250.3909-0.0801-0.01670.2423-0.06940.295450.9871-10.54964.4103
20.26110.20950.12472.32360.95122.27080.0246-0.1045-0.005-0.10920.07480.5022-0.5261-0.38740.00010.3390.049-0.03390.3268-0.01280.367541.434-12.01931.4346
33.55390.0374-1.40090.4227-0.22580.79720.1908-1.7656-0.1127-0.0945-0.49590.2499-1.1040.4081-0.10610.68260.0541-0.10250.0958-0.24860.274948.7162-6.779812.3549
40.67780.2697-0.19420.1075-0.09010.04760.0713-0.69531.39110.39780.73810.1762-0.5217-0.640.01960.9120.2682-0.07520.4143-0.15870.554236.8801-2.43046.0333
50.95020.80270.46770.92761.1622.89380.0525-0.12610.26880.48050.1602-0.50860.00640.62570.00860.3621-0.0065-0.04210.399-0.03650.413153.4068-19.26298.9925
62.7144-0.15931.39561.63140.89825.11560.16180.2476-0.4194-0.27940.2163-0.3110.74740.82960.05540.40360.1274-0.1040.2799-0.14260.351552.6574-29.8609-3.8237
71.78871.23230.18110.95120.01440.23640.0747-0.62471.36630.0250.386-0.2629-1.36230.84540.27670.4611-0.15620.05740.8223-0.24490.475159.1725-14.9722-8.0606
80.59380.04410.59040.85220.74172.34260.24450.0297-0.4364-0.01770.0534-0.50180.76361.24710.01710.48620.2327-0.15640.6054-0.14820.546258.2973-31.1586-0.8521
91.112-0.62241.20821.1188-0.12361.32150.1172-0.5549-0.55070.17120.1166-0.13820.8840.3522-0.00370.46620.0398-0.11250.3324-0.10980.314150.9228-28.65566.332
100.16110.1734-0.12460.207-0.20940.7515-0.2886-0.2309-0.0135-1.00570.2223-0.07560.70410.40350.03151.3296-0.7444-0.2440.9533-0.11020.730839.5769-41.05664.6612
111.1661-0.4881-0.06483.1605-0.81971.22250.1522-0.16890.13910.070.1290.66140.1932-0.77930.00780.2989-0.0894-0.04560.41590.05180.531632.0286-24.55882.172
121.44540.16961.60430.6439-0.3131.8037-0.1598-0.1993-0.31890.14760.23740.52730.6011-0.37350.00150.3508-0.0209-0.05980.31010.00150.393737.5565-24.9121-2.5573
130.8571-0.43990.04690.4172-0.31280.43630.27360.8611-0.3112-0.60310.3241-0.88931.00370.01550.0660.8134-0.0276-0.25960.3703-0.0610.509540.0341-35.3854-13.2644
140.3416-0.26040.25830.8284-0.31340.25450.09430.06890.16630.1505-0.26350.54880.5779-0.7048-0.00220.3298-0.0514-0.00340.3472-0.01260.433935.7948-23.76333.2142
150.4545-0.14780.55040.5402-0.12780.53580.0455-0.0643-0.35020.3094-0.21640.9890.7287-0.73060.00590.6196-0.2914-0.06550.55640.06770.598429.0817-33.38292.9959
160.7991-0.0093-0.21550.7665-0.8640.84240.371-0.5317-0.10260.2291-0.0361-0.35650.1628-0.8916-0.00650.3368-0.0465-0.08660.31190.04110.373239.7159-26.40088.4572
171.496-0.860.57930.495-0.34550.30741.0738-0.4655-0.63660.25750.61350.0714-0.2227-0.6520.15380.91080.20480.31420.8757-0.11561.41633.3261-13.439614.5568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 88 )
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 58 )
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 88 )
9X-RAY DIFFRACTION9chain 'B' and (resid 89 through 98 )
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 104 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 27 )
12X-RAY DIFFRACTION12chain 'C' and (resid 28 through 42 )
13X-RAY DIFFRACTION13chain 'C' and (resid 43 through 58 )
14X-RAY DIFFRACTION14chain 'C' and (resid 59 through 68 )
15X-RAY DIFFRACTION15chain 'C' and (resid 69 through 88 )
16X-RAY DIFFRACTION16chain 'C' and (resid 89 through 99 )
17X-RAY DIFFRACTION17chain 'C' and (resid 100 through 104 )

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