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Yorodumi- PDB-5hrc: Crystal structure of an aspartate/glutamate racemase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hrc | ||||||||||||
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Title | Crystal structure of an aspartate/glutamate racemase in complex with L-aspartate | ||||||||||||
Components | aspartate/glutamate racemase | ||||||||||||
Keywords | ISOMERASE / Aspartate/glutamate racemase / PLP-independent racemase / Racemization mechanism | ||||||||||||
Function / homology | Rossmann fold - #1860 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ASPARTIC ACID / : Function and homology information | ||||||||||||
Biological species | Escherichia coli O157:H7 str. SS52 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å | ||||||||||||
Authors | Liu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Febs Lett. / Year: 2016 Title: Crystal structure and molecular mechanism of an aspartate/glutamate racemase from Escherichia coli O157 Authors: Liu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hrc.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hrc.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hrc_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 5hrc_full_validation.pdf.gz | 484.5 KB | Display | |
Data in XML | 5hrc_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 5hrc_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/5hrc ftp://data.pdbj.org/pub/pdb/validation_reports/hr/5hrc | HTTPS FTP |
-Related structure data
Related structure data | 5hqtSC 5hraC 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: 25990.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 str. SS52 (bacteria) Strain: SS52 / Gene: ygeA, SS52_3985 / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0F6FBL7 #2: Chemical | #3: Chemical | ChemComp-NHE / | #4: 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: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9.5 Details: 1.0 M sodium citrate, 0.1 M CHES, 3.0% D (+)-Sucrose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.989 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 1.765→32.73 Å / Num. obs: 48432 / % possible obs: 91 % / Redundancy: 3.4 % / Net I/σ(I): 20.06 |
Reflection shell | Resolution: 1.765→1.828 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HQT Resolution: 1.765→32.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.26 / Stereochemistry target values: ML
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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: 1.765→32.73 Å
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Refine LS restraints |
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LS refinement shell |
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