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Yorodumi- PDB-7sdp: Replication Initiator Protein REPE54 and cognate DNA sequence wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sdp | ||||||
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Title | Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates. | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Replication Initiator RepE Complex Co-Crystal / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) Eschericia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Ward, A.R. / Snow, C.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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. #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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sdp.cif.gz | 195.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sdp.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/7sdp ftp://data.pdbj.org/pub/pdb/validation_reports/sd/7sdp | HTTPS FTP |
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-Related structure data
Related structure data | 7sozC 7u6kC 7u7oC 7ufxC 7uogC 7ur0C 7uv6C 7uv7C 7uxyC 8d86C 7rvaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 6696.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 6816.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Protein , 1 types, 1 molecules C
#3: 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 |
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-Unknown polymer ... , 2 types, 2 molecules FD
#4: Protein/peptide | Mass: 273.330 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eschericia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#5: Protein/peptide | Mass: 358.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eschericia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 2 types, 49 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM MgCl2, 7% PEG 400, 220 mM Tris HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 16, 2021 |
Radiation | Monochromator: SI (111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.01→37.68 Å / Num. obs: 11131 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.086 / Rrim(I) all: 0.165 / Χ2: 0.48 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.01→3.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1781 / CC1/2: 0.74 / Rpim(I) all: 0.556 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7rva Resolution: 3.01→37.68 Å / SU ML: 0.4527 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.722 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→37.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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