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- PDB-7uv6: Isoreticular, interpenetrating co-crystal of Replication Initiato... -

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Basic information

Entry
Database: PDB / ID: 7uv6
TitleIsoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and scaffold duplex (21mer) containing the cognate REPE54 sequence and an insert duplex (10mer) with guest TAMRA-labelled thymine and G-C rich sequence.
Components
  • DNA (5'-D(*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(*GP*AP*CP*GP*GP*CP*CP*CP*GP*G)-3')
  • DNA (5'-D(*GP*T(TAMRA)P*CP*CP*GP*GP*GP*CP*CP*G)-3')
  • DNA (5'-D(*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 / 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: 2.72 Å
AuthorsOrun, A.R. / Snow, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2003748 United States
CitationJournal: 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.
History
DepositionApr 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 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.title / _citation.year
Revision 1.3May 1, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*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(*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(*GP*AP*CP*GP*GP*CP*CP*CP*GP*G)-3')
F: DNA (5'-D(*GP*T(TAMRA)P*CP*CP*GP*GP*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,84910
Polymers49,7275
Non-polymers1225
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.085, 128.495, 137.260
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*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*A)-3')


Mass: 6367.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*G)-3')


Mass: 6478.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(*GP*AP*CP*GP*GP*CP*CP*CP*GP*G)-3')


Mass: 3071.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(*GP*T(TAMRA)P*CP*CP*GP*GP*GP*CP*CP*G)-3')


Mass: 3061.991 Da / Num. of mol.: 1 / Mutation: TAMRA-labelled thymine2 / 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, 38 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.28 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 300 mM MgCl2, 15% 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 1, 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: 2.72→38.93 Å / Num. obs: 17957 / % possible obs: 99.35 % / Redundancy: 7.3 % / Biso Wilson estimate: 74.98 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06592 / Rpim(I) all: 0.02637 / Rrim(I) all: 0.07107 / Net I/σ(I): 20.25
Reflection shellResolution: 2.72→2.817 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 1779 / CC1/2: 0.739 / Rpim(I) all: 0.4476 / Rrim(I) all: 1.216 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.8.9.3-pre ELmodel building
XDSJune 30, 2021data reduction
XSCALEJune 30, 2021data scaling
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7u6k

7u6k


Resolution: 2.72→38.93 Å / SU ML: 0.4435 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1783 9.96 %
Rwork0.1955 16120 -
obs0.1985 17903 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.19 Å2
Refinement stepCycle: LAST / Resolution: 2.72→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 1259 5 33 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01253277
X-RAY DIFFRACTIONf_angle_d1.47784693
X-RAY DIFFRACTIONf_chiral_restr0.0839509
X-RAY DIFFRACTIONf_plane_restr0.0129388
X-RAY DIFFRACTIONf_dihedral_angle_d27.7247857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.790.46951400.38831231X-RAY DIFFRACTION99.64
2.79-2.880.37711260.34471229X-RAY DIFFRACTION99.78
2.88-2.970.38541370.28961248X-RAY DIFFRACTION99.93
2.97-3.070.32771380.27331202X-RAY DIFFRACTION100
3.07-3.20.30681340.26971229X-RAY DIFFRACTION99.93
3.2-3.340.24071270.21051209X-RAY DIFFRACTION97.73
3.34-3.520.23681460.18781225X-RAY DIFFRACTION99.28
3.52-3.740.26741360.19651249X-RAY DIFFRACTION100
3.74-4.030.24531360.19381227X-RAY DIFFRACTION99.93
4.03-4.430.21161360.16791257X-RAY DIFFRACTION99.93
4.43-5.070.17621370.15581258X-RAY DIFFRACTION100
5.07-6.380.19941440.1671258X-RAY DIFFRACTION100
6.39-38.930.1611460.18271298X-RAY DIFFRACTION96.52
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)
12.8939286589-0.595070526179-0.8033966435210.2776437729120.07343168467672.789281975270.131368071010.414394183399-1.12499974073-0.668409878611-0.08883947779590.05952515949150.2109914694540.0839349843188-0.1309322120540.7599395272680.01891838515460.1189041730020.619036621058-0.3174258875761.06858960387-10.7900310201-47.7259034534-14.5405258901
21.0571921791-0.07622343790821.544827755912.08407729271-0.5320587950864.482590489450.1827909966-0.0218019284235-0.831140803252-0.3155014969980.216295254938-0.4475015967390.4889888251670.533477216276-0.3927372235320.5473391310380.03414938829410.1025913716010.556062812235-0.1752235786061.00273999941-3.35113844521-48.8042864041-6.39279738761
32.3213348231-0.5420075251530.2218495203672.67705890858-0.9008370053362.51756215484-0.0634971262786-0.120326912499-0.660105789044-0.2569670165010.1408826560870.1572893096520.165682226864-0.450393447601-0.09637532588050.421354075608-0.0709483567410.08559857933310.536188927043-0.1545301547450.679482308435-21.1714187143-38.5565030285-5.18844802606
45.046353887530.580400128513-0.415550745076.758818813841.251223061486.979781894790.0139047926099-0.112000741754-0.0884244140001-0.47356193110.01636560921140.8863892458070.143340520419-0.867118182128-0.02199786615190.4214673839250.0322858949219-0.007196573657920.612402062155-0.07075254589170.647469548282-29.8301829-31.2372265518-7.80989802097
54.03753163303-1.18853945492-1.538999312962.902252487210.4586861187661.09891412153-0.226754965388-0.7854940184940.620806391244-0.09185432627040.341924119071-0.596174165162-0.631821386708-0.0369786822227-0.2365486848510.9550088399250.05139610315660.1572895563360.764048032668-0.3325764839210.884505957955-18.0299431948-12.8386835962-4.32909302086
61.64457018781-1.10242585401-1.099836142791.548262004190.6014569992092.011447213090.1239857473920.845755282057-0.11730075358-0.856986487723-0.27219821735-0.7796038853950.1420360098290.42773037791-0.2476258340071.264387100730.09882303997280.4889245730531.16803375389-0.3596181509610.927233433626-2.02871145253-32.6239115745-26.7496641638
72.31581148094-0.881006117745-0.8167221761482.3034289115-0.6888438395881.234010123880.5963314796590.6386524124360.0871062112559-0.550075881648-0.2272553936690.00443898987882-0.06754978406350.348627523529-0.07637915524551.335104417580.1729694618870.4993365633611.24075234538-0.4134523300411.170130271391.37079687656-38.5880473031-30.3335847936
81.986640398590.3601050735951.246866369823.84522983519-1.696526022371.783583739590.01658649715720.1430259104440.862364577556-0.459036217964-0.15117021523-0.276837883447-0.396285046413-0.08319198369890.2375144743760.829417997188-0.01937438184980.2136067843130.676872953966-0.2612560679010.783598653588-13.9800354056-16.0049316255-9.80993911685
91.680307134920.512724284184-0.534929423020.5026707125380.7213392223542.442291150620.0743928369397-0.4807763811210.1618412879980.937872071778-0.01931427399860.440189457617-0.33329838348-0.2528358211670.1654691859791.850906149550.507473160460.245184885281.45048067902-1.031508777721.502736670798.11090267633-59.4789564239-46.5345509189
100.1529933327550.342395019221-0.3161930262582.143628283660.1442684968281.338273292280.240443195767-0.3612425659340.5361072214260.6380196570860.131848143834-0.00127245178169-0.592101460414-0.207354180296-0.008557387190751.896980942930.5885707697570.3424812015691.76890567441-1.146057606091.3887433102110.1014465784-64.0436229626-50.8394741803
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 15 through 89 )CC15 - 892 - 70
22chain 'C' and (resid 90 through 132 )CC90 - 13271 - 102
33chain 'C' and (resid 133 through 208 )CC133 - 208103 - 175
44chain 'C' and (resid 209 through 245 )CC209 - 245176 - 212
55chain 'A' and (resid 0 through 9 )AA0 - 9
66chain 'A' and (resid 10 through 20 )AA10 - 20
77chain 'B' and (resid 22 through 31 )BB22 - 31
88chain 'B' and (resid 32 through 42 )BB32 - 42
99chain 'E' and (resid 21 through 30 )EI21 - 30
1010chain 'F' and (resid 12 through 21 )FJ12 - 21

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