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- PDB-8tit: Isoreticular, interpenetrating co-crystal of Replication Initiato... -

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Basic information

Entry
Database: PDB / ID: 8tit
TitleIsoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and no terminal phosphates.
Components
  • DNA (5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*G)-3')|
  • DNA (5'-D(GP*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP)-3')
  • Replication initiation protein
KeywordsDNA BINDING PROTEIN/DNA / Replication Initiator RepE Complex Co-Crystal / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Initiator Rep protein / Initiator Replication protein, WH1 / Initiator Rep protein, WH2 / 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: 2.84 Å
AuthorsOrun, A.R. / Shields, E.T. / Shrestha, R. / Slaughter, C.K. / Snow, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2003748 United States
Citation
Journal: Acs Nanosci Au / Year: 2024
Title: Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals.
Authors: Orun, A.R. / Slaughter, C.K. / Shields, E.T. / Vajapayajula, A. / Jones, S. / Shrestha, R. / 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
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Aug 14, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*G)-3')|
B: DNA (5'-D(GP*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP)-3')
C: Replication initiation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9639
Polymers49,8173
Non-polymers1466
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-65 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.935, 130.706, 136.176
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

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


Mass: 9483.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(GP*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP)-3')


Mass: 9585.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#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: K-12 / Gene: repE, E, rep, ECOK12F045 / Production host: Escherichia coli (E. coli) / References: UniProt: P03856
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 450 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl

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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: Oct 2, 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: 2.84→38.82 Å / Num. obs: 16128 / % possible obs: 99.51 % / Redundancy: 7.3 % / Biso Wilson estimate: 78.42 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06415 / Rpim(I) all: 0.02564 / Rrim(I) all: 0.06919 / Net I/σ(I): 23.33
Reflection shellResolution: 2.84→2.942 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 1587 / CC1/2: 0.705 / CC star: 0.909 / Rpim(I) all: 0.4627 / Rrim(I) all: 1.271 / % possible all: 99.87

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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 / Resolution: 2.84→38.82 Å / SU ML: 0.3728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2085
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 1602 9.96 %
Rwork0.205 14489 -
obs0.2086 16091 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.83 Å2
Refinement stepCycle: LAST / Resolution: 2.84→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 1263 6 4 3009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01233249
X-RAY DIFFRACTIONf_angle_d1.53744655
X-RAY DIFFRACTIONf_chiral_restr0.09503
X-RAY DIFFRACTIONf_plane_restr0.0143382
X-RAY DIFFRACTIONf_dihedral_angle_d28.412856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.930.35491440.30581293X-RAY DIFFRACTION99.86
2.93-3.040.36371400.31161302X-RAY DIFFRACTION99.93
3.04-3.160.35551440.31311306X-RAY DIFFRACTION100
3.16-3.30.31021460.2311283X-RAY DIFFRACTION98.76
3.3-3.480.2581350.19841303X-RAY DIFFRACTION98.9
3.48-3.690.2461490.22161304X-RAY DIFFRACTION99.59
3.69-3.980.26221460.20241322X-RAY DIFFRACTION99.86
3.98-4.380.22411440.18981325X-RAY DIFFRACTION99.93
4.38-5.010.19941470.17541328X-RAY DIFFRACTION100
5.01-6.310.2331510.18551342X-RAY DIFFRACTION99.93
6.31-38.820.20551560.19471381X-RAY DIFFRACTION97.84
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)
10.0340424085760.05564119749910.01663167040470.0648342925052-0.01784423224470.00824660145-0.103299454346-0.2920335796040.2835804154040.04323431426650.0676614152518-0.00819175926841-0.121124856549-0.135691898267-0.00028400263360.739611592266-0.009681469660820.1304948501470.789542780656-0.3311849439020.782005877768-21.037-7.8371.602
20.07893818832-0.0249315850765-0.0342462021620.01334322512520.01774170476310.03681271094650.03327138203370.351460088037-0.20586531501-0.30775377594-0.111574408518-0.2109847938780.3374178532580.07509258123550.04237894025481.185403746580.009202269017180.5712718041441.19920183942-0.8350410406660.819843386636-0.155-39.997-30.421
30.167008471621-0.0495176650337-0.0886992215830.157577466130.05750069606950.04375051705190.3992705810250.372574718833-0.151699634015-0.218064381170.05908088032160.04137646668660.2404331177850.06497267724980.2887050814471.39485563140.2876804425620.6626017295971.2886882901-0.9373159473061.148938455034.214-44.641-35.441
40.04988421242680.009805622449090.009943066874180.118608620754-0.05779880950080.00463199640786-0.140380240458-0.03283427414730.1842310221430.1512049404410.170492063399-0.116200740142-0.235351715117-0.136626306545-0.02883229783530.743873956873-0.05433746871420.2029260179880.772646236211-0.2338051406710.611170926225-19.378-12.817-3.389
50.130114391412-0.06298039582330.1321267569250.0410283423304-0.0645970789680.1462238377360.08627504664080.063484124692-0.331855768851-0.4065094172240.2525786206180.0337656043326-0.02356707366680.1933812847610.2010515507420.611314413139-0.03174096886810.3000279317020.594034314192-0.51153221731.09013172505-10.853-47.071-14.661
60.00674592358716-0.02904069029490.003016141097230.0331503319973-0.01863336889310.01477685696670.120970688148-0.0842745882383-0.376320694166-0.1394579794280.17916405877-0.1504496711610.07384811605720.03673368549270.0001117187101040.645393264222-0.007605309927350.2337981813270.69356638481-0.1448832572031.15705872917-3.455-48.229-6.236
70.0672536999-0.10687061764-0.01212316557740.124143052146-0.01160535023470.254609727301-0.0148492336996-0.31210640772-0.337016567858-0.137709250550.04431031110750.184952974009-0.143264251819-0.355582633211-0.0228660748961-0.0387033223246-0.0969310219140.2925769594340.496831055836-0.3407148114190.838408860889-21.418-38.159-5.226
80.02252672317090.00752317010985-0.006436226195820.0201474263310.0079714886110.00875343519038-0.04743873805590.080554410496-0.0909456123127-0.1144436949770.1951655292940.106044811914-0.0426998951863-0.1013890531726.312962917660.533766156313-0.1017702565180.04941282659860.62634626101-0.1978798775910.675583784354-30.229-31.061-7.712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:16 )A2 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:32 )A17 - 32
3X-RAY DIFFRACTION3( CHAIN B AND RESID 2:16 )B2 - 16
4X-RAY DIFFRACTION4( CHAIN B AND RESID 17:32 )B17 - 32
5X-RAY DIFFRACTION5( CHAIN C AND RESID 15:89 )C15 - 89
6X-RAY DIFFRACTION6( CHAIN C AND RESID 90:132 )C90 - 132
7X-RAY DIFFRACTION7( CHAIN C AND RESID 133:208 )C133 - 208
8X-RAY DIFFRACTION8( CHAIN C AND RESID 209:245 )C209 - 245

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