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

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Basic information

Entry
Database: PDB / ID: 6mmc
TitleCarbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to ADP
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'-DIPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 30, 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)12,0434
Polymers11,4841
Non-polymers5593
Water1,22568
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)36,12812
Polymers34,4523
Non-polymers1,6769
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8480 Å2
ΔGint-98 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.632, 68.632, 89.052
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-202-

SO4

31A-343-

HOH

41A-345-

HOH

51A-358-

HOH

61A-363-

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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5II98
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5 M Ammonium Sulfate

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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 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.42→49.44 Å / Num. obs: 24053 / % possible obs: 100 % / Redundancy: 37.8 % / Biso Wilson estimate: 23.554052012 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.024 / Rrim(I) all: 0.0108 / Net I/av σ(I): 22.6 / Net I/σ(I): 22.6
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 36.3 % / Num. unique obs: 1180 / CC1/2: 0.38 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MM2

6mm2


Resolution: 1.42→49.44 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1984 --
Rwork0.1717 --
obs-24048 99.96 %
Refinement stepCycle: LAST / Resolution: 1.42→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 33 68 799
LS refinement shellResolution: 1.42→1.471 Å
RfactorNum. reflection% reflection
Rfree0.3775 --
Rwork0.3114 --
obs-2345 99.91 %
Refinement TLS params.Method: refined / Origin x: 2.2964 Å / Origin y: 28.2526 Å / Origin z: -5.9576 Å
111213212223313233
T0.2999 Å20.009 Å20.0124 Å2-0.2728 Å20.0094 Å2--0.0847 Å2
L1.8112 °2-0.1175 °20.7692 °2-1.2543 °20.0298 °2--1.2225 °2
S-0.0172 Å °-0.0867 Å °-0.127 Å °-0.0798 Å °-0.013 Å °-0.0033 Å °0.2211 Å °0.1085 Å °0.0347 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 104
2X-RAY DIFFRACTION1allA201 - 368

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