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- PDB-7spm: Replication Initiator Protein REPE54 and cognate DNA sequence wit... -

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Basic information

Entry
Database: PDB / ID: 7spm
TitleReplication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (30 mg/mL EDC, 12 hours, 2 doses).
Components
  • DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)-3')
  • DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')
  • RepB family plasmid replication initiator protein
KeywordsDNA BINDING PROTEIN/DNA / Replication Initiator RepE Complex Co-Crystal / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA replication initiation / DNA-directed DNA polymerase activity
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) / RepB family plasmid replication initiator protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsWard, A.R. / Snow, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2003748 United States
Citation
Journal: Crystals / Year: 2022
Title: Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA
Authors: Orun, A.R. / 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
DepositionNov 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*A)-3')
B: DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')
C: RepB family plasmid replication initiator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2864
Polymers44,2623
Non-polymers241
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-31 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.817, 80.174, 74.723
Angle α, β, γ (deg.)90.000, 122.899, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 6696.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*A)-3')


Mass: 6816.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Protein RepB family plasmid replication initiator protein / RepE / RepE protein / Replication initiation protein / Replication initiation protein FIA / ...RepE / RepE protein / Replication initiation protein / Replication initiation protein FIA / Replication initiation protein RepE / Replication initiation protein of repFIA / FIA / FIA replicon / Replication protein


Mass: 30749.053 Da / Num. of mol.: 1 / Mutation: R118P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: repE, RepE, repE_1, repE_2, A9P13_27925, ACN81_13795, AKG29_00005, AM270_25025, AM446_00510, AM465_27515, APX88_12585, B9N33_25510, BANRA_05159, BANRA_05459, BANRA_05682, BANRA_05685, BE930_ ...Gene: repE, RepE, repE_1, repE_2, A9P13_27925, ACN81_13795, AKG29_00005, AM270_25025, AM446_00510, AM465_27515, APX88_12585, B9N33_25510, BANRA_05159, BANRA_05459, BANRA_05682, BANRA_05685, BE930_02070, BE963_00170, BFD68_26000, BIU72_26315, BK334_12915, BON69_00085, BON86_02490, BTQ06_15345, BvCmsKSNP073_00547, BvCmsKSNP081_03109, C5F73_28740, C6669_28055, CCZ17_26065, CDL37_25390, CUB99_27055, D0X26_27580, D2188_23935, D6C57_20535, D6T60_26250, D9G11_25395, D9J60_24770, DL545_01395, DLU82_26460, DM102_26130, DMZ50_25125, DN808_25760, DNQ45_17165, DP277_27365, E0L04_25075, E4K51_24545, E5P24_21725, E5S56_18100, EA191_27055, EA214_24280, EA233_23655, EA834_24495, EC3234A_223c00190, ECTO124_05352, EGT48_00285, EIZ93_24320, EJC75_00275, ELT22_23490, ELT31_24090, ELT31_26285, ELT33_22145, ELU82_24155, ELU85_22525, ELV00_24275, ELV13_22345, ELV22_21715, ELV22_26415, ELV24_23180, ELV24_26400, ELX56_23450, ELX56_26570, ELX68_22815, ELX68_25985, ELX70_23725, ELX70_27680, ELX79_25360, ELX79_27900, ELX83_21670, ELX83_26905, ELY23_22635, ELY23_25820, ELY24_18745, ELY24_28685, ELY48_20420, ELY48_27905, ELY50_22820, ELY50_26360, EPS70_23590, EQ823_22980, EQ830_17775, ERS085362_04815, ERS150873_04643, EVY14_01415, ExPECSC065_01123, F0L67_01685, F7O57_26240, FAF34_003215, FKO60_21690, FVA71_27640, G3565_27065, G4276_24945, G4280_26215, G5603_23890, G5632_20220, G5697_22865, G5V60_25015, GE057_22565, GE087_25865, GE096_23180, GE400_25540, GE558_24730, GKE29_21080, GKE58_20235, GKE60_20510, GKE79_19945, GKE87_19350, GQY14_24020, GRC73_23425, HGR17_18615, HGR87_25030, HGR88_23710, HGS97_17250, HH117_25695, HH456_004544, HH814_004957, HIO03_005020, HIZ44_004944, HJ359_004520, HJI79_004024, HJL93_004672, HJM89_004053, HJT66_004466, HKA14_004545, HL186_24195, HLI97_004832, HMT01_25475, HMT08_23785, HNV94_24925, HNX16_24825, HNX34_21985, HPE39_26560, HR075_24855, HV055_25390, HV303_25935, HVW09_26465, HVW60_23575, HVW98_24555, HVX24_22925, HVX51_24935, HVY93_24645, HVZ71_26895, IB283_25495, IPF_37, pCTXM15_EC8_00107, RCS105_pI0165, RCS57_p0140, RCS59_P0063, SAMEA4370330_00165, SAMEA4370365_00054, SY51_26335, WP4S17E03_P11650, WP4S18E08_P10410, YDC107_5106
Production host: Escherichia coli (E. coli) / References: UniProt: Q0E856
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 70 mM MgCl2, 5% PEG 400, and 220 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: Apr 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: 3.28→36.91 Å / Num. obs: 8468 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 94.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.073 / Rrim(I) all: 0.14 / Χ2: 0.5 / Net I/σ(I): 5.4
Reflection shellResolution: 3.28→3.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1724 / CC1/2: 0.93 / Rpim(I) all: 0.42 / Rrim(I) all: 0.811 / Χ2: 0.55 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4092refinement
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: 7rva

7rva


Resolution: 3.28→36.91 Å / SU ML: 0.4781 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.8467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 448 5.36 %
Rwork0.2009 7909 -
obs0.2037 8357 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.22 Å2
Refinement stepCycle: LAST / Resolution: 3.28→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 861 1 7 2619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01462789
X-RAY DIFFRACTIONf_angle_d1.62643960
X-RAY DIFFRACTIONf_chiral_restr0.0832437
X-RAY DIFFRACTIONf_plane_restr0.0116363
X-RAY DIFFRACTIONf_dihedral_angle_d26.1475666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.540.36241440.30162547X-RAY DIFFRACTION95.56
3.54-4.730.28211620.23922645X-RAY DIFFRACTION99.12
4.73-36.910.20711420.15572717X-RAY DIFFRACTION99.41
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)
13.99008625638-1.43756456688-0.08328015607794.66419194991-0.5997672878722.949615159650.5105272947180.686886971924-0.8370309088390.791363494056-0.2904602815481.479448569861.106186336460.6649385823520.2243314236451.016719878320.3856675427440.08996861241751.507818948130.105309849381.9938085526638.8630544863-28.525087019513.9616451511
22.66234633364-1.2882532796-1.333651213250.4642039415720.7118451908590.651380882398-0.4448769403670.7669184243-2.154654699880.2100551128680.3535101523571.84436673339-0.304836193421-1.492127826790.6713421461571.033832645110.5092605819970.09953788782861.764704462650.5013186705492.554756546511.3671137501-7.2310585039715.4369780833
32.902001845231.350479615440.8071737350355.17756653846-3.861807706394.1761104034-0.3984195927520.761931381899-0.0338897813593-1.308569079830.3988311726490.2418443422170.57323759182-0.404353724262-0.5102587536031.388192610350.814399315460.2319900628892.015232838330.5289582322672.084455571988.518186864792.0061808547715.8592014899
44.90121777292-1.93992586116-3.087369191793.825875708952.178512056618.30280262165-0.5723632840210.555408312615-3.187698361910.9064008466520.5021918123851.15427566351-0.392288140111-1.386172076920.8751579344481.168713972550.3030636613530.08167285427611.303780555250.5347202774853.411809702713.5951430061-15.635463685516.501607237
53.343908150690.123008615328-3.108859241578.08447193143-2.96586940324.56542789560.3428229037740.114874917249-3.460217562160.1220496633680.6773285346442.617312082072.022435539260.0103861674568-0.3583845848210.8396086227530.2709417814770.04857675990361.014837374410.06711414570732.0329803731330.7362246049-19.77753122513.4406699762
66.700170760960.83813174373-3.530733131130.306171227101-0.3483395192182.58924774356-1.120191595560.645275459185-1.952987565950.704378356270.7130992298810.3325007243911.481393918661.129511536140.472059254111.417920694860.5330579849390.12650128761.502821242560.0465736773262.0871650378445.0219619542-34.759115497414.2505047837
74.103413291-1.63661876971.012657560533.118283066070.05293591801231.620543223910.1342748135440.6524200859081.15444325387-0.05579449427060.1759680817431.12898295761-0.833940239358-0.305136860596-0.3111049294881.006045646620.2291411363220.09330839070830.8535541351730.3195012365290.92539650469128.63577133895.2723821201413.8396234179
85.928201922750.09198807794580.4222486888871.789391943040.2341863573386.931756395530.459753761591-2.396578602591.655505311330.208461285078-0.1765488391080.831174909621-1.47071664898-0.04534019676340.2213517873231.059454957020.2064634378790.2347238610030.7318369357480.01607719775641.0341255726931.56624432586.4866417787324.7283801262
97.24766666881-0.0986269612337-2.934516821821.229993818171.083744532464.713743806010.5861336596850.681109179070.532486234909-0.221095437613-0.3523506522690.46567111107-0.6770704831390.74101832768-0.2256590316820.8542494306110.2463699083370.07392754233851.050479561780.3212622923540.61451753296542.662452922-3.4226804520410.4862590156
104.267449492581.88867195616-0.3736050228822.818862797930.2911570304893.20924108436-0.4691339004211.97912690188-0.1737222335-0.835725235391-0.0149340710390.7569422966870.184948115720.321737702081-0.339480079740.9026587234360.27005380651-0.2382206491871.442821022240.3296527064420.6881907679144.9725879523-11.221665991.55295385403
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 )AA1 - 10
22chain 'A' and (resid 11 through 22 )AA11 - 22
33chain 'B' and (resid 23 through 27 )BB23 - 27
44chain 'B' and (resid 28 through 32 )BB28 - 32
55chain 'B' and (resid 33 through 37 )BB33 - 37
66chain 'B' and (resid 38 through 44 )BB38 - 44
77chain 'C' and (resid 14 through 89 )CC14 - 891 - 74
88chain 'C' and (resid 90 through 132)CC90 - 13275 - 108
99chain 'C' and (resid 133 through 208 )CC133 - 208109 - 185
1010chain 'C' and (resid 209 through 247 )CC209 - 247186 - 226

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