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- PDB-7uv7: Isoreticular, interpenetrating co-crystal of Replication Initiato... -

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Basic information

Entry
Database: PDB / ID: 7uv7
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 T-A 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*TP*AP*AP*TP*T)-3')
  • DNA (5'-D(*GP*T(TAMRA)P*AP*AP*TP*TP*AP*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: 3.02 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 17, 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*TP*AP*AP*TP*T)-3')
F: DNA (5'-D(*GP*T(TAMRA)P*AP*AP*TP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7476
Polymers49,7225
Non-polymers241
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.493, 131.392, 132.464
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*TP*AP*AP*TP*T)-3')


Mass: 3084.041 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*AP*AP*TP*TP*AP*CP*CP*G)-3')


Mass: 3044.017 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, 9 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / 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: 3.22 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM MgCl2, 30% 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: 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: 3.02→37.85 Å / Num. obs: 12804 / % possible obs: 96.74 % / Redundancy: 6.9 % / Biso Wilson estimate: 80.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07113 / Rpim(I) all: 0.03014 / Rrim(I) all: 0.07743 / Net I/σ(I): 20.98
Reflection shellResolution: 3.02→3.128 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.6448 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 1284 / CC1/2: 0.91 / Rpim(I) all: 0.2514 / Rrim(I) all: 0.6925 / % possible all: 99.69

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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: 3.02→37.85 Å / SU ML: 0.4805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 1253 9.99 %
Rwork0.2312 11291 -
obs0.2351 12544 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.32 Å2
Refinement stepCycle: LAST / Resolution: 3.02→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 1259 1 8 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053241
X-RAY DIFFRACTIONf_angle_d0.83334639
X-RAY DIFFRACTIONf_chiral_restr0.0547503
X-RAY DIFFRACTIONf_plane_restr0.0061379
X-RAY DIFFRACTIONf_dihedral_angle_d27.8419850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.140.47851460.47491276X-RAY DIFFRACTION99.65
3.14-3.280.3251330.25921238X-RAY DIFFRACTION98
3.28-3.460.2871370.24611237X-RAY DIFFRACTION96.29
3.46-3.670.34891330.31341229X-RAY DIFFRACTION96.39
3.67-3.960.39351320.29671159X-RAY DIFFRACTION90.72
3.96-4.350.24141410.21651266X-RAY DIFFRACTION97.78
4.36-4.980.2131410.17921289X-RAY DIFFRACTION100
4.98-6.270.21821500.18551317X-RAY DIFFRACTION99.93
6.27-37.850.22931400.20371280X-RAY DIFFRACTION92.87
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)
11.84631309636-0.942892708641-1.511482039912.480046783810.6191840685661.301691790680.107609501204-0.3477392983820.4156041908310.1618239858160.0792997137501-0.408157893241-0.2365856207370.0317619438395-0.3645199951851.086900534680.1896171304510.4494275608570.845084488011-0.569198028941.26620781854-16.1566980614-15.8414755178-4.195966976
21.85896262849-0.404531963932-0.3870838802280.9687095099560.4483325348292.286669679380.01173008666530.776490465704-0.426940453843-0.728489185464-0.0764423401818-0.601006965380.3057463368080.499407944791-0.001006889988941.51722150.3564173062730.4937689931341.08616388734-0.316433358070.694249682203-1.17251012876-35.5159211365-27.5831987661
32.14184087691-1.25299491593-0.8090399979261.974654147910.419377567970.2991584706510.1806811076010.1420660017320.0328542630292-0.2295432684380.211332794086-0.3575654361490.02165604396650.2444482595490.09137259980971.73957746050.3667737979210.6996099456490.919149738058-0.6741923173020.9917141085891.03970393435-38.728094929-29.3604560332
43.71929050093-0.847981085504-0.2341571849873.543519239830.9115707395592.693221459390.0906792065029-0.4509621119470.931468323137-0.02053278363710.1591920199280.00628546216086-0.74549085771-0.5362916764930.1385212247331.025663571410.2417915735920.566877070690.480108339369-0.4848661143621.02355520732-13.8748289041-17.589441417-7.21148993789
53.659637934110.0291162985543-1.884976522263.547938339820.4129063857337.471864639330.1361922983950.260654705059-0.90288019341-0.8026788260920.01730915728770.3194997882630.756816676245-0.1542199673470.2848997279360.7875862536980.0354612983768-0.01767261903560.556823874559-0.3295800725910.672241491641-10.7703828451-49.6518533961-14.8466840303
62.314225872140.680422051504-0.3001161309733.0039535461-1.652458246118.895100340190.120027615124-0.181339907319-0.525058004048-0.4096275653720.254794928426-0.3833247564491.09152979570.944086856056-0.3694688113520.6327713729860.0935400331234-0.007357823632920.56323698465-0.1814807753870.61698701559-3.14025865417-50.972360087-6.67101089269
73.11573314082-0.499393658411-0.4807974840133.49440171234-1.00088877252.280913817420.252056001405-0.180762393469-0.579722019826-0.154047849284-0.2077753159160.523330508323-0.0549349235676-0.4984933871060.02849323766330.333098218238-0.05205529382090.03826793502520.479414807777-0.2079855058230.714811483183-20.784795282-40.3504657234-5.24410723873
86.33612007179-0.736076647001-2.205123069727.178747772393.557403236692.88407539807-0.0876865611790.239744007694-0.1728249470780.176341753918-0.1337789450941.080983297590.468472608266-0.8906926009390.4512544698740.292357117790.0437314483185-0.03049259898170.613328306405-0.09916661833820.918746005254-29.574091152-32.9006498492-7.14182406615
91.31740301644-0.378748873039-0.1140133463062.416063489791.163637505881.80426285005-0.00510753400072-0.02083735491060.1093840695640.3531904016950.056705101933-0.138619991176-0.4782211304290.0276188290566-0.2264397948522.399964705970.6595339711930.7030427725661.50382707563-1.879605007251.545794781358.09231067944-61.1661387496-45.3992673926
100.1306725967440.2805470525680.04675005365280.6792138761310.1033176134370.02695285659060.026869534507-0.02355487621340.1547720890080.199287768855-0.0844023925645-0.085233069678-0.108711127036-0.08863947168290.09177571543542.596911840310.6382867738120.6335365797741.90310615884-1.143276976271.682948591329.84330686977-67.2930952438-49.1138168976
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 10 )AA0 - 10
22chain 'A' and (resid 11 through 20 )AA11 - 20
33chain 'B' and (resid 22 through 32 )BB22 - 32
44chain 'B' and (resid 33 through 42 )BB33 - 42
55chain 'C' and (resid 14 through 89 )CC14 - 891 - 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 21 through 30 )EE21 - 30
1010chain 'F' and (resid 12 through 21 )FF12 - 21

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