+Open data
-Basic information
Entry | Database: PDB / ID: 7vqj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of NDM-1 in complex with hydrolyzed 1u. | ||||||
Components | Metallo-beta-lactamase NDM-1 | ||||||
Keywords | METAL BINDING PROTEIN / NDM-1 | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Xie, H.X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of NDM-1 in complex with hydrolyzed 1u. Authors: Xie, H.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vqj.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vqj.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vqj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vqj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7vqj_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 7vqj_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vqj ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vqj | HTTPS FTP |
-Related structure data
Related structure data | 5ypnS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25631.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-1 / Production host: Klebsiella pneumoniae (bacteria) / References: UniProt: A0A0A7Y424 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.67 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 16684 / % possible obs: 99.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 31.49 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.095 / Net I/σ(I): 6.42 |
Reflection shell | Resolution: 2.44→2.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 784 / Rpim(I) all: 0.408 / % possible all: 95.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YPN Resolution: 2.45→38.06 Å / SU ML: 0.321 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.548 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→38.06 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|