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Yorodumi- PDB-3mr1: Crystal structure of methionine aminopeptidase from Rickettsia pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mr1 | ||||||
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Title | Crystal structure of methionine aminopeptidase from Rickettsia prowazekii | ||||||
Components | Methionine aminopeptidase | ||||||
Keywords | HYDROLASE / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID / protease / aminopeptidase / metalloenzyme / epidemic typhus / lice-born pathogen | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis Similarity search - Function | ||||||
Biological species | Rickettsia prowazekii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2017 Title: Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents. Authors: Helgren, T.R. / Chen, C. / Wangtrakuldee, P. / Edwards, T.E. / Staker, B.L. / Abendroth, J. / Sankaran, B. / Housley, N.A. / Myler, P.J. / Audia, J.P. / Horn, J.R. / Hagen, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mr1.cif.gz | 437.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mr1.ent.gz | 355.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/3mr1 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/3mr1 | HTTPS FTP |
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-Related structure data
Related structure data | 3mx6C 1xnzS C: citing same article (ref.) 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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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27905.914 Da / Num. of mol.: 4 / Fragment: UNP residues 3-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Gene: map, Q9ZCD3, RP824 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZCD3, methionyl aminopeptidase |
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-Non-polymers , 5 types, 1091 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: 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: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M SPG buffer pH 8.0, 25% PEG 1500 with 20% ethylene glycol as cryoprotectant, 29 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.4 Å / Num. obs: 73427 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.91 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.32 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.6 / % possible all: 84 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1xnz Resolution: 2→42.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.768 / SU ML: 0.099 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.352 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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 |
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