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- PDB-6czf: The structure of E. coli PurF in complex with ppGpp-Mg -

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Basic information

Entry
Database: PDB / ID: 6czf
TitleThe structure of E. coli PurF in complex with ppGpp-Mg
ComponentsAmidophosphoribosyltransferase
KeywordsTRANSFERASE / PurF / ppGpp
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.949 Å
AuthorsWang, B. / Grant, R.A. / Laub, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM082899 United States
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Affinity-based capture and identification of protein effectors of the growth regulator ppGpp.
Authors: Wang, B. / Dai, P. / Ding, D. / Del Rosario, A. / Grant, R.A. / Pentelute, B.L. / Laub, M.T.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Amidophosphoribosyltransferase
B: Amidophosphoribosyltransferase
C: Amidophosphoribosyltransferase
D: Amidophosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,1518
Polymers222,8964
Non-polymers1,2554
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18740 Å2
ΔGint-44 kcal/mol
Surface area69750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.293, 115.339, 156.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Amidophosphoribosyltransferase / / ATase / Glutamine phosphoribosylpyrophosphate amidotransferase / GPATase


Mass: 55723.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: purF, b2312, JW2309 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG16, amidophosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Drops containing 2 uL of protein (25 mg.ml in 20 mM HEPES pH 7.4, 150 mM NaCl, 1 mM TCEP, 5 mM ppGpp, 15 mM MgCl2) were mixed with 2 uL of well solution (0.1 M HEPES pH 7.4, 24% PEG-3350, 4% isopropanol.)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.949→100 Å / Num. obs: 141205 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.33 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Χ2: 0.937 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.985.11.49269030.5070.721.6620.44699
1.98-2.025.81.19469880.6830.5381.3130.44699.8
2.02-2.066.11.05869760.7330.4631.1570.461100
2.06-2.15.90.84369950.7960.3760.9250.47999.9
2.1-2.156.30.769970.8570.3020.7640.48899.9
2.15-2.26.90.59170200.9170.2430.640.514100
2.2-2.256.80.47569910.9280.1960.5150.523100
2.25-2.316.70.42770220.9470.1770.4630.55100
2.31-2.386.70.34469950.9650.1430.3730.597100
2.38-2.466.60.28370430.9720.1190.3080.62799.9
2.46-2.546.10.23270230.9770.1020.2540.70899.9
2.54-2.656.40.19770240.9860.0840.2140.774100
2.65-2.776.90.16270710.990.0660.1750.85299.9
2.77-2.916.80.13570600.9920.0560.1461.0299.9
2.91-3.16.70.11170550.9930.0460.1211.224100
3.1-3.336.20.09370930.9950.040.1011.49299.9
3.33-3.676.80.0871280.9960.0330.0871.787100
3.67-4.26.80.06771440.9970.0270.0721.99599.9
4.2-5.296.30.05572030.9980.0230.061.9399.8
5.29-1006.50.04874740.9980.0210.0521.43599.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ecj

1ecj


Resolution: 1.949→48.642 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.85
RfactorNum. reflection% reflection
Rfree0.2409 1982 1.41 %
Rwork0.2163 --
obs0.2166 140744 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.42 Å2 / Biso mean: 52.1422 Å2 / Biso min: 23.34 Å2
Refinement stepCycle: final / Resolution: 1.949→48.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15577 0 192 380 16149
Biso mean--38.59 44.27 -
Num. residues----1985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9491-1.99780.43091300.37649634976498
1.9978-2.05180.3361340.324598229956100
2.0518-2.11220.3271490.291298149963100
2.1122-2.18040.30881280.270698699997100
2.1804-2.25830.32911490.2638985810007100
2.2583-2.34870.29181470.26987210019100
2.3487-2.45560.31491410.2498990710048100
2.4556-2.58510.32251410.2487989110032100
2.5851-2.7470.2931400.243992110061100
2.747-2.95910.3071430.2385994610089100
2.9591-3.25680.2461430.2348996310106100
3.2568-3.7280.21371430.20281000410147100
3.728-4.69620.19041440.16911008710231100
4.6962-48.65750.19281500.1841101741032498

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