+Open data
-Basic information
Entry | Database: PDB / ID: 1hkh | ||||||
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Title | unligated gamma lactamase from an Aureobacterium species | ||||||
Components | GAMMA LACTAMASE | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE / CO-FACTOR FREE HALOPEROXIDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MICROBACTERIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Line, K. / Isupov, M.N. / Littlechild, J.A. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2004 Title: The crystal structure of a (-) gamma-lactamase from an Aureobacterium species reveals a tetrahedral intermediate in the active site. Authors: Line, K. / Isupov, M.N. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hkh.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hkh.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hkh ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hkh | HTTPS FTP |
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-Related structure data
Related structure data | 1hl7C 1broS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.32713, 0.77924, -0.53457), Vector: |
-Components
#1: Protein | Mass: 30878.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MICROBACTERIUM (bacteria) / Description: CHIROTECH CULTURE COLLECTION / Plasmid: PTRC99 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8GJP7 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | NAMED CO-FACTOR FREE HALOPEROXI | |
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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: 4.72 Å3/Da / Density % sol: 73.73 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7.5 / 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8482 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8482 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→11 Å / Num. obs: 119247 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 24.76 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 11 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.23 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.73 Å / Lowest resolution: 11 Å / % possible obs: 100 % / Redundancy: 11.39 % / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BRO Resolution: 1.73→11 Å / SU B: 1.055 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→11 Å
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Refinement | *PLUS Rfactor Rfree: 0.158 / Rfactor Rwork: 0.144 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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