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- PDB-7rmw: Crystal structure of B. subtilis PurR bound to ppGpp -

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Basic information

Entry
Database: PDB / ID: 7rmw
TitleCrystal structure of B. subtilis PurR bound to ppGpp
ComponentsPur operon repressor
KeywordsDNA BINDING PROTEIN / PurR / ppGpp / transcription / regulator / DNA binding
Function / homology
Function and homology information


negative regulation of purine nucleobase metabolic process / nucleoside metabolic process / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Pur operon repressor / Bacterial purine repressor, N-terminal / Bacterial purine repressor, N-terminal / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Pur operon repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus.
Authors: Anderson, B.W. / Schumacher, M.A. / Yang, J. / Turdiev, A. / Turdiev, H. / Schroeder, J.W. / He, Q. / Lee, V.T. / Brennan, R.G. / Wang, J.D.
History
DepositionJul 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pur operon repressor
B: Pur operon repressor
C: Pur operon repressor
D: Pur operon repressor
E: Pur operon repressor
F: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,97810
Polymers187,5656
Non-polymers2,4134
Water1,72996
1
A: Pur operon repressor
B: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7284
Polymers62,5222
Non-polymers1,2062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-40 kcal/mol
Surface area22980 Å2
MethodPISA
2
C: Pur operon repressor
D: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1253
Polymers62,5222
Non-polymers6031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-31 kcal/mol
Surface area23180 Å2
MethodPISA
3
E: Pur operon repressor
F: Pur operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1253
Polymers62,5222
Non-polymers6031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.264, 90.969, 98.708
Angle α, β, γ (deg.)62.750, 75.360, 78.530
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pur operon repressor


Mass: 31260.902 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: purR, B4122_4510, B4417_1788, BS16045_00058, CFD21_22225, ETA10_00295, ETL41_13190, FAL52_19670, FIU26_15290, SC09_Contig28orf00392
Production host: Escherichia coli (E. coli) / References: UniProt: A0A063X7Y1
#2: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


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


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 18% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→80.5 Å / Num. obs: 62863 / % possible obs: 95.2 % / Redundancy: 3 % / CC1/2: 0.997 / Rpim(I) all: 0.039 / Rsym value: 0.055 / Net I/σ(I): 7.8
Reflection shellResolution: 2.45→2.52 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4598 / CC1/2: 0.94 / Rpim(I) all: 0.277 / Rsym value: 0.377

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P4A

1p4a


Resolution: 2.45→80.494 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1725 2.74 %
Rwork0.1945 61138 -
obs0.1957 62863 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 343.81 Å2 / Biso mean: 79.7247 Å2 / Biso min: 24.75 Å2
Refinement stepCycle: final / Resolution: 2.45→80.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12178 0 144 96 12418
Biso mean--176.62 67.65 -
Num. residues----1581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.52210.30481300.2764459885
2.5221-2.60350.31481450.2513516496
2.6035-2.69660.27981440.2405511597
2.6966-2.80450.28551460.234515196
2.8045-2.93220.30211460.2467515496
2.9322-3.08680.31731460.2499519797
3.0868-3.28020.29391460.2444519497
3.2802-3.53350.30691470.2201518397
3.5335-3.8890.26141430.1922508296
3.889-4.45180.19851440.1677511295
4.4518-5.60850.18451450.16513096
5.6085-80.4940.20871430.1685505895
Refinement TLS params.Method: refined / Origin x: -19.3248 Å / Origin y: -75.7119 Å / Origin z: -39.5334 Å
111213212223313233
T0.2704 Å2-0.0018 Å2-0.0251 Å2-0.3205 Å2-0.001 Å2--0.2933 Å2
L0.1315 °20.0542 °2-0.0721 °2-0.4223 °2-0.0249 °2--0.2102 °2
S0.0147 Å °0.0047 Å °0.0179 Å °-0.0061 Å °-0.0223 Å °-0.0361 Å °0.0754 Å °-0.0334 Å °-0.0068 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 275
2X-RAY DIFFRACTION1allB2 - 273
3X-RAY DIFFRACTION1allC2 - 274
4X-RAY DIFFRACTION1allD2 - 274
5X-RAY DIFFRACTION1allE2 - 274
6X-RAY DIFFRACTION1allF2 - 273
7X-RAY DIFFRACTION1allM301
8X-RAY DIFFRACTION1allT302
9X-RAY DIFFRACTION1allZ305
10X-RAY DIFFRACTION1allY303
11X-RAY DIFFRACTION1allS1 - 96

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