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Yorodumi- PDB-1o5k: Crystal structure of Dihydrodipicolinate synthase (TM1521) from T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o5k | |||||||||
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Title | Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution | |||||||||
Components | 4-hydroxy-tetrahydrodipicolinate synthase | |||||||||
Keywords | LYASE / TM1521 / DIHYDRODIPICOLINATE SYNTHASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | |||||||||
Function / homology | Function and homology information (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of Dihydrodipicolinate synthase (TM1521) from Thermotoga maritima at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o5k.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o5k.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o5k_validation.pdf.gz | 413.8 KB | Display | wwPDB validaton report |
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Full document | 1o5k_full_validation.pdf.gz | 416.1 KB | Display | |
Data in XML | 1o5k_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 1o5k_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/1o5k ftp://data.pdbj.org/pub/pdb/validation_reports/o5/1o5k | HTTPS FTP |
-Related structure data
Related structure data | 1dhpS 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 on special symmetry positions |
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Details | THE AUTHORS' STATE THAT ANALYTICAL ULTRACENTRIFUGATION SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. SEE DOI:10.1042/BJ20060771 |
-Components
#1: Protein | Mass: 33957.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: dapA, TM_1521 / Plasmid: MH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 References: UniProt: Q9X1K9, 4-hydroxy-tetrahydrodipicolinate synthase #2: Chemical | ChemComp-CA / | #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: 2.12 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5 Details: 28% PEG-400, 0.1M Sodium HEPES pH 7.5, 0.2M Calcium chloride dihydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2003 / Details: bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→50 Å / Num. all: 68682 / Num. obs: 68682 / % possible obs: 100 % / Redundancy: 4.25 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.096 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 1.74 % / Mean I/σ(I) obs: 1.04 / Num. unique all: 5042 / Rsym value: 0.712 / % possible all: 65.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DHP Resolution: 1.8→35.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.605 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. CONTINUOUS RESIDUAL DENSITY WAS MODELED AS WATER CHAINS. 3. HEPTAVALENT CALCIUM AND THREE WATERS WERE MODELED INTO PROMINENT DENSITY ...Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. CONTINUOUS RESIDUAL DENSITY WAS MODELED AS WATER CHAINS. 3. HEPTAVALENT CALCIUM AND THREE WATERS WERE MODELED INTO PROMINENT DENSITY ON A SPECIAL POSITION MEDIATING A CRYSTAL CONTACT. CALCIUM WAS SELECTED OVER MAGNESIUM BECAUSE: (A) APPARENTLY HEPTAVALENT COORDINATION, (B) BETTER RFREE, (C) THE B-FACTOR AGREED WITH THAT OF SURROUNDING ATOMS, AND (D) BOND LENGTHS. 4. ACTIVE SITE RESIDUE LYS161 IS COVALENTLY MODIFIED WITH PYRUVATE. THERE IS OTHER, POORLY DEFINED DENSITY ADJACENT TO THIS, IN THE ACTIVE SITE, BUT HAS BEEN MODELED AS WATER. 5. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: 25.358 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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: 1 - 294 / Label seq-ID: 13 - 306
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