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- PDB-7ril: Crystal structure of hairpin polyamide Py-Im 1 bound to 5' CCTGACCAGG -

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Basic information

Entry
Database: PDB / ID: 7ril
TitleCrystal structure of hairpin polyamide Py-Im 1 bound to 5' CCTGACCAGG
Components
  • non-template DNA
  • template DNA
KeywordsDNA / Polyamide / small molecule / DNA binding molecule / anticancer agent
Function / homologyChem-5N0 / ACETATE ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Model detailsRNA polymerase II, 5-guanidinohydantoin, elongation complex, DNA lesion
AuthorsOh, J. / Dervan, P.B. / Wang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Authors: Oh, J. / Jia, T. / Xu, J. / Chong, J. / Dervan, P.B. / Wang, D.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_nat
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-template DNA
B: template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5084
Polymers6,0912
Non-polymers1,4172
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-4 kcal/mol
Surface area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.910, 33.910, 47.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: DNA chain non-template DNA


Mass: 3029.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain template DNA


Mass: 3061.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-5N0 / 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid


Mass: 1358.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C64H75N23O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM Tris pH 7.5, 24% 2-methyl-2,4-pentanediol (MPD) and 35 mM calcium acetate, with 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.65→47.46 Å / Num. obs: 7383 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 47.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 10.6 / Num. measured all: 65231 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.689.12.02336283980.4850.7042.1440.9100
8.89-47.469.20.027486530.9990.010.0284399.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal duplex

Resolution: 1.8→29.367 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 45.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 307 5.44 %
Rwork0.2034 5341 -
obs0.2052 5648 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.98 Å2 / Biso mean: 63.3494 Å2 / Biso min: 40.54 Å2
Refinement stepCycle: final / Resolution: 1.8→29.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 103 17 524
Biso mean--73.5 62 -
Num. residues----20
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8002-2.26790.36631280.31572700
2.2679-29.3670.21931790.192641
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)
13.3854-1.51180.41419.1187-0.15333.5125-0.6058-0.41330.34561.10270.76070.511-0.1371-0.1401-0.12890.48030.25380.00020.53710.0240.49868.2229-0.8825-0.6345
24.8489-0.0444-0.11632.4323-0.47892.7378-0.1351-0.0258-0.1285-0.16230.0528-0.0555-0.15740.08280.08350.66320.12190.04910.3474-0.01270.38219.2038-1.9811-1.0945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 10 )B1 - 10

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