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Yorodumi- PDB-7t1q: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t1q | ||||||
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Title | Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid | ||||||
Components | Succinyl-diaminopimelate desuccinylase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DapE | ||||||
Function / homology | Function and homology information succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii ATCC 17978 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Pshenychnyi, S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid. Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Pshenychnyi, S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t1q.cif.gz | 313.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t1q.ent.gz | 253.6 KB | Display | PDB format |
PDBx/mmJSON format | 7t1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/7t1q ftp://data.pdbj.org/pub/pdb/validation_reports/t1/7t1q | HTTPS FTP |
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-Related structure data
Related structure data | 5uejS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41468.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii ATCC 17978 (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 Gene: dapE, A1S_2810 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Magic References: UniProt: A3M8H2, succinyl-diaminopimelate desuccinylase |
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-Non-polymers , 5 types, 355 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.94 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Protein: 10.6 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3, 2mM N6-Me-L,L-SDAP; Screen: Classics II (D5), 0.1M Sodium acetate pH 4.5, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97848 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97848 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 50400 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.043 / Rrim(I) all: 0.151 / Rsym value: 0.145 / Χ2: 1.068 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2507 / CC1/2: 0.756 / CC star: 0.928 / Rpim(I) all: 0.607 / Χ2: 1.009 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uej Resolution: 2.25→29.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.067 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.64 Å2 / Biso mean: 53.815 Å2 / Biso min: 22.46 Å2
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Refinement step | Cycle: final / Resolution: 2.25→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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