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Yorodumi- PDB-8jzd: Crystal structure of Escherichia coli NarJ in complex with the si... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jzd | |||||||||
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Title | Crystal structure of Escherichia coli NarJ in complex with the signal peptide of E. coli NarG | |||||||||
Components |
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Keywords | CHAPERONE / redox enzyme maturation protein / NarJ subfamily / signal peptide | |||||||||
Function / homology | Function and homology information nitrate reductase (quinone) / NarGHI complex / nitrate reductase (quinone) activity / nitrate metabolic process / metallochaperone activity / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / chaperone-mediated protein complex assembly ...nitrate reductase (quinone) / NarGHI complex / nitrate reductase (quinone) activity / nitrate metabolic process / metallochaperone activity / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / chaperone-mediated protein complex assembly / nitrate assimilation / unfolded protein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Song, W.S. / Kim, J.H. / Namgung, B. / Cho, H.Y. / Oh, H.B. / Yoon, S.I. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG. Authors: Song, W.S. / Kim, J.H. / Namgung, B. / Cho, H.Y. / Shin, H. / Oh, H.B. / Ha, N.C. / Yoon, S.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jzd.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jzd.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 8jzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jzd_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 8jzd_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 8jzd_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 8jzd_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jzd ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jzd | HTTPS FTP |
-Related structure data
Related structure data | 8jzcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 166 / Label seq-ID: 1 - 166
NCS oper: (Code: givenMatrix: (0.484383861145, 0.874280994641, 0.0317020105334), (-0.859790785871, 0.482426023097, -0.167406501579), (-0.161654197576, 0.0538319110657, 0.985378123239)Vector: -31. ...NCS oper: (Code: given Matrix: (0.484383861145, 0.874280994641, 0.0317020105334), Vector: |
-Components
#1: Protein | Mass: 21781.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: narJ, b1226, JW1217 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AF26 #2: Protein/peptide | Mass: 1956.337 Da / Num. of mol.: 2 / Fragment: signal peptide / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P09152, nitrate reductase (quinone) |
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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: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 17555 / % possible obs: 98.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 52.97 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 2.45→2.49 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 871 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model Resolution: 2.45→28.88 Å / SU ML: 0.3492 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.6935 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: 76.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→28.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.461118709957 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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