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- PDB-8d8m: Isoreticular, interpenetrating co-crystal of Replication Initiato... -

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Entry
Database: PDB / ID: 8d8m
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 grown in a calcium chloride crystallization solution.
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*GP*A)-3')
  • DNA (5'-D(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*GP*A)-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: 3.1 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: To Be Published
Title: Designed crystalline assemblies of protein and DNA enable site-specific installation of a guest protein, DNA, and small molecule.
Authors: Orun, A.R. / Shields, E.T. / Dmytriw, S. / Vajapayajula, A. / 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
DepositionJun 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 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

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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*GP*A)-3')
B: DNA (5'-D(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*GP*A)-3')
C: Replication initiation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5245
Polymers50,4443
Non-polymers802
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-47 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.322, 133.189, 134.645
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*GP*A)-3')


Mass: 9796.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(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*GP*A)-3')


Mass: 9898.351 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: K12 / Gene: repE, E, rep, ECOK12F045 / Production host: Escherichia coli (E. coli) / References: UniProt: P03856
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 400 mM MgCl2, 24% PEG 400, and 80 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: Dec 16, 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: 3.1→37.98 Å / Num. obs: 12285 / % possible obs: 98.77 % / Redundancy: 7 % / Biso Wilson estimate: 75.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1145 / Rpim(I) all: 0.04712 / Rrim(I) all: 0.124 / Net I/σ(I): 14.18
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.279 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 1202 / CC1/2: 0.887 / Rpim(I) all: 0.504 / Rrim(I) all: 1.376 / % possible all: 99.83

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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: 3.1→37.98 Å / SU ML: 0.434 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 1211 9.94 %
Rwork0.2235 10968 -
obs0.2268 12179 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.41 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 1273 2 3 3014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01393261
X-RAY DIFFRACTIONf_angle_d1.57784679
X-RAY DIFFRACTIONf_chiral_restr0.0879508
X-RAY DIFFRACTIONf_plane_restr0.0132382
X-RAY DIFFRACTIONf_dihedral_angle_d27.6339865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.43611360.36011204X-RAY DIFFRACTION99.78
3.22-3.370.2811230.20421201X-RAY DIFFRACTION98
3.37-3.550.34661320.28391181X-RAY DIFFRACTION98.35
3.55-3.770.29981310.2891201X-RAY DIFFRACTION99.18
3.77-4.060.32591370.28951184X-RAY DIFFRACTION95.72
4.06-4.470.24551300.20741212X-RAY DIFFRACTION99.93
4.47-5.110.23051360.1811243X-RAY DIFFRACTION99.93
5.12-6.440.231430.19321241X-RAY DIFFRACTION100
6.44-37.980.19431430.19251301X-RAY DIFFRACTION98.63
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)
10.138609566145-0.0192084553259-0.06658899081680.03412817121020.05898723689060.0779410150423-0.1433650211260.557268655020.42543955443-0.3954895652440.03594891892060.144905714492-0.2962341277510.0505605995564-0.002478346666030.9276792702670.208146038312-0.01482365232830.9040276917140.3538219016470.917541504157-17.4898713995-0.314835786494-56.3793542081
20.0990712801763-0.08540893751070.04444140544690.0641134823396-0.01220877647720.0163020297177-0.0259025614901-0.186498017156-0.346063623610.391203194036-0.0471322126368-0.04062781647150.325761706590.108152492107-0.05735339409231.506241512770.6241955365230.04493373586430.7347566565061.210726260241.348890108220.830101922101-33.2377167757-22.1608661668
30.0684547261596-0.0716477508688-0.05429537158820.07458543995180.09708341325340.08192364434550.24234792119-0.39120257959-0.4759579334120.3628668411880.0137031167525-0.2129923258560.3369832028420.214419468110.03622393609251.44813608630.6358664447-0.231807719430.8666820515340.8779056837411.214172942641.27189257337-32.7315071292-25.5216981354
40.06337950083740.0198990215414-0.02332307844160.008409410193830.01988686332410.0578012980352-0.1267129532470.3194458905840.400518437198-0.5751166261440.0599132379010.160068565528-0.6895509127480.0799112074621-0.02122113568631.35099675570.263768314703-0.02161207892470.7109498408330.2858241361580.773243241628-19.79314566762.85726352832-56.526292633
50.03366775338120.02759237326350.05149006943630.0776615690633-0.06512809752540.193801793623-0.0680034737553-0.319340206152-0.16092844404-0.102271814468-0.189468006313-0.1562474401380.39642286568-0.013721092909-0.2778863166460.2949573029660.224140301547-0.1683546761780.8713093383650.7194249139470.426152251757-10.7257269906-14.8457863151-18.479058121
60.01153870575570.01461611818650.03316035117480.009592797361810.03029069286220.0512867828147-0.0471012979815-0.326448894061-0.08741239933410.116237733088-0.136199678518-0.06617908122140.2579327767890.0936983797548-0.02441143500730.3500838454910.2582180696740.01772450633110.9827789721050.1470955158350.423000001543-3.35047955651-6.39877808281-17.0733918534
70.05844900678910.0904971803232-0.01279016311740.524007721460.01835712415440.0275162297972-0.235659941615-0.5541436830450.11105092954-0.2940056705930.004273707966690.2531471545590.0591074412017-0.0809957693159-0.09488654010310.1755437584870.1385892977950.0477809994280.7096282858810.1766470470110.42008708367-20.8749982477-5.41710209586-27.9043181712
80.0376459264752-0.0161303175530.004389423464820.006749313379440.004050323019950.0148320371425-0.01539091567910.005004360710680.0954349455499-0.07886321432840.02443118600390.1048413538870.0283724243137-0.157604494874-0.0001366471153630.432362714122-0.008160683943620.02187385400380.4738267639260.1002341127090.636481408566-29.4583840139-7.91911237355-35.4132803193
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 18 )AA2 - 18
22chain 'A' and (resid 19 through 33 )AA19 - 33
33chain 'B' and (resid 3 through 19 )BB3 - 19
44chain 'B' and (resid 20 through 34 )BB20 - 34
55chain 'C' and (resid 15 through 89 )CC15 - 891 - 68
66chain 'C' and (resid 90 through 132 )CC90 - 13269 - 100
77chain 'C' and (resid 133 through 208)CC133 - 208101 - 173
88chain 'C' and (resid 209 through 245 )CC209 - 245174 - 210

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