+Open data
-Basic information
Entry | Database: PDB / ID: 1nmt | ||||||
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Title | N-MYRISTOYL TRANSFERASE FROM CANDIDA ALBICANS AT 2.45 A | ||||||
Components | N-MYRISTOYL TRANSFERASE | ||||||
Keywords | MYRISTYLATION / ANTIFUNGAL TARGET / COA / TRANSFERASE / ACYLTRANSFERASE | ||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.45 Å | ||||||
Authors | Weston, S.A. / Pauptit, R.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of the anti-fungal target N-myristoyl transferase. Authors: Weston, S.A. / Camble, R. / Colls, J. / Rosenbrock, G. / Taylor, I. / Egerton, M. / Tucker, A.D. / Tunnicliffe, A. / Mistry, A. / Mancia, F. / de la Fortelle, E. / Irwin, J. / Bricogne, G. / Pauptit, R.A. #1: Journal: To be Published Title: Refinement of N-Myryistoyl Transferase at 2.45A Authors: Rowsell, S. / Pauptit, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nmt.cif.gz | 252 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmt.ent.gz | 204.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmt_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
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Full document | 1nmt_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 1nmt_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 1nmt_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmt ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 45421.566 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) References: UniProt: P30418, glycylpeptide N-tetradecanoyltransferase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Compound details | APOENZYME STRUCTURE. ENZYME BINDS MYRISTYL COA (PRESUMABLY IN GROOVE) PLUS SUBSTRATE PROTEIN N- ...APOENZYME STRUCTURE. ENZYME BINDS MYRISTYL COA (PRESUMABLY | |
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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: 3.8 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1995 / Details: VERTICALLY-FOCUSED PT-COATED MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20.85 Å / Num. obs: 72615 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.318 / % possible all: 95.5 |
Reflection shell | *PLUS % possible obs: 95.5 % |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.45→20.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: BULK SOLVENT MODEL USED. 18 GLYCEROL MOLECULES INCLUDED AS FRA 1 - 18.
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Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→20.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAIN / Rms dev Biso : 7.26 Å2 / Weight Biso : 3 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.315 |