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Open data
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Basic information
Entry | Database: PDB / ID: 1nm2 | ||||||
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Title | Malonyl-CoA:ACP Transacylase | ||||||
![]() | malonyl CoA:acyl carrier protein malonyltransferase | ||||||
![]() | TRANSFERASE / ALPHA/BETA HYDROLASE-LIKE CORE / ACETATE BOUND TO ACTIVE SITE MIMICKING A MALONYL GROUP | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keatinge-Clay, A.T. / Shelat, A.A. / Savage, D.F. / Tsai, S. / Miercke, L.J.W. / O'Connell III, J.D. / Khosla, C. / Stroud, R.M. | ||||||
![]() | ![]() Title: Catalysis, Specificity, and ACP Docking Site of Streptomyces coelicolor Malonyl-CoA:ACP Transacylase Authors: Keatinge-Clay, A.T. / Shelat, A.A. / Savage, D.F. / Tsai, S. / Miercke, L.J.W. / O'Connell III, J.D. / Khosla, C. / Stroud, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 50 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1mlaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32246.709 Da / Num. of mol.: 1 / Fragment: Malonyl-CoA:ACP Transacylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P72391, [acyl-carrier-protein] S-malonyltransferase | ||
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#2: Chemical | ChemComp-NI / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG 4000, sodium acetate, ammonium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2002 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.81 Å / Num. obs: 17011 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 16.7 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 54 / Limit l min: 0 / Observed criterion F max: 1282968.78 / Observed criterion F min: 12.5 / Rsym value: 0.081 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2268 / Rsym value: 0.412 / % possible all: 85.6 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 65258 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 85.6 % / Rmerge(I) obs: 0.412 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MLA Resolution: 2→48.81 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 51.2305 Å2 / ksol: 0.389125 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.24 Å2 / Biso mean: 22.73 Å2 / Biso min: 11.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→48.81 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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