+Open data
-Basic information
Entry | Database: PDB / ID: 4aee | ||||||
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Title | CRYSTAL STRUCTURE OF MALTOGENIC AMYLASE FROM S.MARINUS | ||||||
Components | ALPHA AMYLASE, CATALYTIC REGION | ||||||
Keywords | HYDROLASE / HYPERTHERMOSTABLE / CYCLODEXTRIN HYDROLASE / GH13 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STAPHYLOTHERMUS MARINUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Jung, T.Y. / Park, C.H. / Yoon, S.M. / Park, S.H. / Park, K.H. / Woo, E.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Association of Novel Domain in Active Site of Archaic Hyperthermophilic Maltogenic Amylase from Staphylothermus Marinus. Authors: Jung, T.Y. / Li, D. / Park, J.T. / Yoon, S.M. / Tran, P.L. / Oh, B.H. / Janecek, S. / Park, S.G. / Woo, E.J. / Park, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aee.cif.gz | 287.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aee.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 4aee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aee_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 4aee_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 4aee_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 4aee_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4aee ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4aee | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 82575.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOTHERMUS MARINUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 References: UniProt: A3DM60, glucan 1,4-alpha-maltohydrolase #2: 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: 2.32 Å3/Da / Density % sol: 46.98 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 12% PEG 4K, 2% ISO-PROPANOL, 0.1 M ADA PH 6.5, 0.1 M LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→49.55 Å / Num. obs: 65614 / % possible obs: 85.6 % / Observed criterion σ(I): 2.13 / Redundancy: 8.2 % / Biso Wilson estimate: 34.35 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.12 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.19 / % possible all: 72.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→49.554 Å / SU ML: 0.28 / σ(F): 2.13 / Phase error: 23.23 / Stereochemistry target values: ML Details: IN BOTH CHAIN A AND B, THE RESIDUES FROM 656-659 AND 671-678 REGIONS ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.207 Å2 / ksol: 0.347 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→49.554 Å
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Refine LS restraints |
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LS refinement shell |
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