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Yorodumi- PDB-3erp: Structure of IDP01002, a putative oxidoreductase from and essenti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3erp | ||||||
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Title | Structure of IDP01002, a putative oxidoreductase from and essential gene of Salmonella typhimurium | ||||||
Components | Putative oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES OF NIH CONTRACT NUMBER HHSN272200700058C / predicted oxidoreductase / essential gene / Salmonella / molecular replacement / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information methylglyoxal catabolic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Singer, A.U. / Minasov, G. / Evdokimova, E. / Brunzelle, J.S. / Kudritska, M. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2017 Title: Structural and biochemical studies of novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol. Authors: Kim, T. / Flick, R. / Brunzelle, J. / Singer, A. / Evdokimova, E. / Brown, G. / Joo, J.C. / Minasov, G.A. / Anderson, W.F. / Mahadevan, R. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3erp.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3erp.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 3erp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3erp_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 3erp_full_validation.pdf.gz | 489.4 KB | Display | |
Data in XML | 3erp_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 3erp_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3erp ftp://data.pdbj.org/pub/pdb/validation_reports/er/3erp | HTTPS FTP |
-Related structure data
Related structure data | 5t79C 1zsxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39862.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: no TEV cleavage Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: STM2406 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q8ZNA1 |
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-Non-polymers , 6 types, 868 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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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: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 6.5 Details: crystallized in 0.2 M Calcium Acetate, 9% PEG8000 and 0.1 M Sodium Cacodylate. Cryoprotected with 25% ethylene glycol., pH 6.5, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2008 / Details: mirrors |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 136598 / Num. obs: 132754 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.08 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.62 / Num. unique all: 13638 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body ...Starting model: PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A. Resolution: 1.55→29.96 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.166 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.404 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.554→1.594 Å / Total num. of bins used: 20
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