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Yorodumi- PDB-8aud: Structure of peptidoglycan hydrolase Cg1735 from Corynebacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aud | ||||||
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Title | Structure of peptidoglycan hydrolase Cg1735 from Corynebacterium glutamicum, orthorhombic crystal form | ||||||
Components | Cell wall-associated hydrolases (Invasion-associated proteins) | ||||||
Keywords | CELL CYCLE / bacterial cell division / peptidoglycan hydrolysis / regulatory protein | ||||||
Function / homology | NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / hydrolase activity / Cell wall-associated hydrolases (Invasion-associated proteins) Function and homology information | ||||||
Biological species | Corynebacterium glutamicum ATCC 13032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Gaday, Q. / Wehenkel, A.M. / Alzari, P.M. | ||||||
Funding support | France, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales. Authors: Gaday, Q. / Megrian, D. / Carloni, G. / Martinez, M. / Sokolova, B. / Ben Assaya, M. / Legrand, P. / Brule, S. / Haouz, A. / Wehenkel, A.M. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aud.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aud.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 8aud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/8aud ftp://data.pdbj.org/pub/pdb/validation_reports/au/8aud | HTTPS FTP |
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-Related structure data
Related structure data | 8au6C 8aucSC S: Starting model for refinement 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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-Components
#1: Protein | Mass: 61858.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and ...Details: The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK).,The register is unknown for helix 344-362 in chain A and helix 350-365 in chain B. These residues were modeled as poly-alanine (UNK). Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Gene: Cgl1538 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQA0 |
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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: 4.97 Å3/Da / Density % sol: 75.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 2.4 M (NH4)2SO4, 0.1 M Na3 citrate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98112 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98112 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→61.54 Å / Num. obs: 15441 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.992 / Rpim(I) all: 0.117 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 4.5→5.03 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4293 / CC1/2: 0.931 / Rpim(I) all: 0.342 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AUC Resolution: 4.5→61.54 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→61.54 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 |
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