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Yorodumi- PDB-1o5i: Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (... -
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-Basic information
Entry | Database: PDB / ID: 1o5i | ||||||
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Title | Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution | ||||||
Components | 3-oxoacyl-(acyl carrier protein) reductase | ||||||
Keywords | OXIDOREDUCTASE / TM1169 / 3-OXOACYL-(ACYL CARRIER PROTEIN) REDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / NADP binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o5i.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o5i.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o5i_validation.pdf.gz | 886.6 KB | Display | wwPDB validaton report |
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Full document | 1o5i_full_validation.pdf.gz | 909.5 KB | Display | |
Data in XML | 1o5i_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 1o5i_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/1o5i ftp://data.pdbj.org/pub/pdb/validation_reports/o5/1o5i | HTTPS FTP |
-Related structure data
Related structure data | 1i01S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 3
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-Components
#1: Protein | Mass: 27686.096 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1169 / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0Q1, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | ChemComp-NAD / | #3: 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: 2.54 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5 Details: 20% PEG-6000, 0.1M citric acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.972386 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2002 / Details: flat mirror |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972386 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41.17 Å / Num. all: 31633 / Num. obs: 31633 / % possible obs: 85.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 51.32 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2231 / Rsym value: 0.229 / % possible all: 42.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD, MOLECULAR REPLACEMENT Starting model: 1i01 Resolution: 2.5→41.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.212 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.807 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER ...Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER SUBUNITS, ELECTRON DENSITY IS SUGGESTIVE BUT TOO WEAKTO JUSTIFY FITTING NAD, PRESUMABLY DUE TO DIFFERING CRYSTAL CONTACTS. 3. THE DISULFIDE BOND (37-54) HAS NEGATIVE DIFFERENCE DENSITY IN ALL SUBUNITS, PRESUMABLY DUE TO RADIATION DAMAGE. 4. NCS IS BROKEN AT RESIDUES 54-61 AND 84/137, DUE TO CRYSTAL CONTACTS.
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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: 15.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→41.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 4 - 237 / Label seq-ID: 16 - 249
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