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- PDB-7ur0: Isoreticular, interpenetrating co-crystal of Replication Initiato... -

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Basic information

Entry
Database: PDB / ID: 7ur0
TitleIsoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate REPE54 sequence and an additional T-A rich sequence, respectively.
Components
  • DNA (5'-D(*AP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*A)-3')
  • DNA (5'-D(A*GP*AP*CP*GP*GP*TP*AP*AP*TP*T)-3')
  • DNA (5'-D(A*GP*TP*AP*AP*TP*TP*AP*CP*CP*G)-3')
  • DNA (5'-D(A*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)-3')
  • Replication initiation protein
KeywordsDNA BINDING PROTEIN/DNA / Replication Initiator RepE Complex Co-Crystal / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Initiator Rep protein, WH2 / Initiator Rep protein / Initiator Replication protein, WH1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication initiation protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsOrun, A.R. / Snow, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2003748 United States
Citation
Journal: Acs Nano / Year: 2023
Title: Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds.
Authors: Orun, A.R. / Shields, E.T. / Dmytriw, S. / Vajapayajula, A. / Slaughter, C.K. / Snow, C.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*A)-3')
B: DNA (5'-D(A*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)-3')
C: Replication initiation protein
E: DNA (5'-D(A*GP*AP*CP*GP*GP*TP*AP*AP*TP*T)-3')
F: DNA (5'-D(A*GP*TP*AP*AP*TP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0247
Polymers50,9755
Non-polymers492
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-48 kcal/mol
Surface area19500 Å2
Unit cell
Length a, b, c (Å)74.407, 127.493, 135.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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DNA chain , 4 types, 4 molecules ABEF

#1: DNA chain DNA (5'-D(*AP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*A)-3')


Mass: 6680.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(A*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)-3')


Mass: 6791.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(A*GP*AP*CP*GP*GP*TP*AP*AP*TP*T)-3')


Mass: 3397.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(A*GP*TP*AP*AP*TP*TP*AP*CP*CP*G)-3')


Mass: 3357.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules C

#3: Protein Replication initiation protein / Protein E / Protein rep / Protein F4


Mass: 30749.053 Da / Num. of mol.: 1 / Mutation: R118P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: repE, E, rep, ECOK12F045 / Production host: Escherichia coli (E. coli) / References: UniProt: P03856

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Non-polymers , 2 types, 10 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.15 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 120 mM MgCl2, 20% PEG 400, 100 mM Tris HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 30, 2021
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→38.61 Å / Num. obs: 10028 / % possible obs: 97.79 % / Redundancy: 6.9 % / Biso Wilson estimate: 71.06 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.3851 / Rpim(I) all: 0.1595 / Rrim(I) all: 0.4175 / Net I/σ(I): 5.91
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 967 / CC1/2: 0.904 / Rpim(I) all: 0.4899 / Rrim(I) all: 1.314 / % possible all: 96.94

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.8.9.3-pre ELmodel building
XDSJan 31, 2020data reduction
XSCALEJan 31, 2020data scaling
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7u6k

7u6k


Resolution: 3.3→38.61 Å / SU ML: 0.4318 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.275 973 9.9 %
Rwork0.2281 8852 -
obs0.2331 9825 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.41 Å2
Refinement stepCycle: LAST / Resolution: 3.3→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 1275 2 8 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413264
X-RAY DIFFRACTIONf_angle_d0.77474678
X-RAY DIFFRACTIONf_chiral_restr0.0486508
X-RAY DIFFRACTIONf_plane_restr0.006381
X-RAY DIFFRACTIONf_dihedral_angle_d28.0134860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.470.31671350.25911221X-RAY DIFFRACTION96.44
3.47-3.690.35061420.25591266X-RAY DIFFRACTION99.51
3.69-3.980.32441320.25851239X-RAY DIFFRACTION97.79
3.98-4.380.34521410.22021242X-RAY DIFFRACTION97.05
4.38-5.010.24361330.22251269X-RAY DIFFRACTION97.7
5.01-6.30.28861410.23311268X-RAY DIFFRACTION98.05
6.31-38.610.21351490.20531347X-RAY DIFFRACTION98.68
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)
13.22086603087-1.40871865698-2.944805972092.391234444721.473398050143.290134376670.207466927168-0.1053203250440.5627184685940.09487063150430.100409281408-0.922547692975-0.2846977014710.120321101826-0.4507787395940.9697516469020.2557806379980.2670095662420.66180744605-0.523624313231.04395377805-17.7573397482-14.0802966467-4.95823366542
20.4691250228370.220582359890.5428612167980.5568080087710.5186418473191.183431238410.005780625238780.542363878195-0.236954942004-0.756588687735-0.193118177429-0.4825619291140.3223224840170.394852702602-0.1659117935841.404482287770.5043849616390.6162863144341.36141586775-0.7256351739161.18663691384-2.50600503965-33.9770445474-28.0644118475
32.91010754754-1.37819990096-0.8589244966346.199733652231.288914045132.062751183980.1104932926510.1053789912650.152594219022-0.005586030151310.0321882901703-0.134832189444-0.2845683431240.0406279458393-0.1638163627761.353687702990.133028522440.3293969239041.14500700296-0.8201459541371.258669384671.47228298916-40.541816382-30.9454679359
43.91266275659-0.573352392585-0.2373151705943.746402051580.7996602460262.85744405180.1466063117570.07662441506320.759415167832-0.2512109654210.115145215201-0.504395060752-0.634862711714-0.486140394508-0.2270271820440.8908816747690.0542588505610.5066448029830.585551238122-0.3418705035950.660326249368-14.2706628913-17.1015588471-11.3498440278
51.95245802351-0.520911029381-0.4613768046411.891138821731.243988427454.41842640115-0.05556667774150.328606494498-0.796859602224-0.6876462486420.002633865852110.1800770393640.634778445511-0.01941846153150.6891866115560.7870232837840.04767161488640.2153022048660.527498133472-0.6333621373390.9118656786-10.7840048947-47.7898148634-14.3364076705
61.574002492810.5007835643390.9259725252562.5205476615-1.594806651075.105355830950.198552608123-0.123634349634-0.430541373513-0.4969786336050.263896757481-0.3912844902390.7386809807370.628261161656-0.3798745429820.4665190363870.0367877192434-0.101575155140.391603585583-0.3320152295071.29885957853-3.10178007941-48.4570074003-6.52163715844
72.68419550632-0.394751154046-0.1356225031962.69108344987-0.6683924870842.4210247310.1628175085480.0587701074237-0.7468400747970.055340287585-0.2222137079340.2210976207330.0446141402692-0.1185848889210.006905436581730.315747247471-0.03271717808520.2484217775890.42984943721-0.3227335775680.856697554405-21.2045191771-38.7668439259-5.04380415284
86.56877859516-0.590338263532-2.324107944275.588871361222.067792853179.22082288353-0.3755201302420.455285424893-0.3094692754610.1141572791940.02837065816220.7814874860520.575236288974-0.7069865947280.4714295801950.399955134477-0.03148354324350.2578125555010.495171315804-0.1413760048340.73600100103-30.2922997687-31.8606988119-7.05045255774
91.58911637507-0.658266987202-0.6595938556672.265214730831.440870357282.667261838720.224529766346-0.2071556504190.1994026312180.7629888171790.0182683586336-0.0101455548425-0.518295615670.14316228017-0.3772699167241.852813346530.2827363783040.2761644799611.62529767639-0.9046866848531.066120490117.39214206716-58.5909533833-45.9490996869
100.291141736061-0.0842503861386-0.09831998668051.546254863780.7402716565290.3713341508630.0736757228301-0.0008585777224690.1910678511820.2550527160590.0364596640168-0.235234316969-0.0110432057231-0.149696939139-0.03118160147411.985374630040.4264547093080.3616814680491.43812372512-0.7953880031781.276187545559.11138178321-64.3783357259-51.3957782473
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 10 )AA-1 - 10
22chain 'A' and (resid 11 through 20 )AA11 - 20
33chain 'B' and (resid 21 through 30 )BB21 - 30
44chain 'B' and (resid 31 through 42 )BB31 - 42
55chain 'C' and (resid 15 through 89 )CC15 - 892 - 70
66chain 'C' and (resid 90 through 132 )CC90 - 13271 - 102
77chain 'C' and (resid 133 through 208 )CC133 - 208103 - 175
88chain 'C' and (resid 209 through 245 )CC209 - 245176 - 212
99chain 'E' and (resid 20 through 30 )EF20 - 30
1010chain 'F' and (resid 11 through 21 )FG11 - 21

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