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- PDB-4rx6: Structure of B. subtilis GlnK-ATP complex to 2.6 Angstrom -

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Basic information

Entry
Database: PDB / ID: 4rx6
TitleStructure of B. subtilis GlnK-ATP complex to 2.6 Angstrom
ComponentsNitrogen regulatory PII-like protein
KeywordsTRANSCRIPTION / PII protein
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / 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 ...Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / 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 PII-like protein
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5994 Å
AuthorsSchumacher, M.A. / Cuthbert, B. / Tonthat, N. / Chinnam, N.G. / Whitfill, T.
CitationJournal: Genes Dev. / Year: 2015
Title: Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Authors: Schumacher, M.A. / Chinnam, N.B. / Cuthbert, B. / Tonthat, N.K. / Whitfill, T.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrogen regulatory PII-like protein
B: Nitrogen regulatory PII-like protein
D: Nitrogen regulatory PII-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7266
Polymers40,2043
Non-polymers1,5223
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-45 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.200, 103.200, 77.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nitrogen regulatory PII-like protein


Mass: 13401.415 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: nrgB, BSU36520 / Plasmid: pET15-b / Production host: Escherichia coli (E. coli) / References: UniProt: Q07428
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.599→44.7 Å / Num. all: 15175 / Num. obs: 14872 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R25

4r25


Resolution: 2.5994→44.687 Å / FOM work R set: 0.7556 / SU ML: 0.49 / σ(F): 0 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 1481 9.96 %random
Rwork0.2241 ---
obs0.2289 14872 98.79 %-
all-15175 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.994 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 124.88 Å2 / Biso mean: 50.63 Å2 / Biso min: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.2362 Å2-0 Å20 Å2
2---1.2362 Å2-0 Å2
3---2.4725 Å2
Refinement stepCycle: LAST / Resolution: 2.5994→44.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 93 42 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112683
X-RAY DIFFRACTIONf_angle_d1.5413631
X-RAY DIFFRACTIONf_chiral_restr0.079422
X-RAY DIFFRACTIONf_plane_restr0.006447
X-RAY DIFFRACTIONf_dihedral_angle_d23.4461029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5994-2.69230.4671320.37521207133991
2.6923-2.80010.39911450.34611331147699
2.8001-2.92750.39491430.307213361479100
2.9275-3.08180.34621420.27213351477100
3.0818-3.27490.33551500.236213471497100
3.2749-3.52760.31771550.244813411496100
3.5276-3.88250.32941460.2481338148498
3.8825-4.44380.18811530.165913581511100
4.4438-5.5970.17781510.157813741525100
5.597-44.69350.23391640.21891424158899

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