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Yorodumi- PDB-3zh4: crystal structure of S. pneumoniae Hungary 19A MurA1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zh4 | ||||||
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Title | crystal structure of S. pneumoniae Hungary 19A MurA1 in complex with citrate | ||||||
Components | UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / MURA | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytosol Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gutierrez-Fernandez, J. / Hermoso, J.A. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 Title: Heteroresistance to Fosfomycin is Predominant in Streptococcus Pneumoniae and Depends on Mura1 Gene. Authors: Engel, H. / Gutierrez-Fernandez, J. / Fluckiger, C. / Martinez-Ripoll, M. / Muhlemann, K. / Hermoso, J.A. / Hilty, M. / Hathaway, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zh4.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zh4.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zh4_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 3zh4_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 3zh4_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3zh4_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zh4 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zh4 | HTTPS FTP |
-Related structure data
Related structure data | 3zh3C 1nawS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45102.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: HUNGARY 19A-6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: B1IBM3, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-FLC / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.9 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE, PH 5.6, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.2 Å / Num. obs: 32208 / % possible obs: 99.7 % / Observed criterion σ(I): 2.3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NAW Resolution: 1.8→45.241 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE NOT INCLUDED IN THE MODEL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.241 Å
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Refine LS restraints |
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LS refinement shell |
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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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