+Open data
-Basic information
Entry | Database: PDB / ID: 2g4l | ||||||
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Title | Anomalous substructure of hydroxynitrile lyase | ||||||
Components | (S)-acetone-cyanohydrin lyase | ||||||
Keywords | LYASE / anomalous substructure of hydroxynitrile lyase | ||||||
Function / homology | Function and homology information (S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity Similarity search - Function | ||||||
Biological species | Hevea brasiliensis (rubber tree) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUE (A CME 94 ) AND RESIDUE (A GLU 95 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.78. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4l.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4l.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 2g4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g4l_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 2g4l_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 2g4l_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2g4l_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4l ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4l | HTTPS FTP |
-Related structure data
Related structure data | 2g4hC 2g4iC 2g4jC 2g4kC 2g4mC 2g4nC 2g4oC 2g4pC 2g4qC 2g4rC 2g4sC 2g4tC 2g4uC 2g4vC 2g4wC 2g4xC 2g4yC 2g4zC 2g51C 2g52C 2g55C 2illC 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 on special symmetry positions |
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-Components
#1: Protein | ( Mass: 29338.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / References: UniProt: P52704, EC: 4.1.2.39 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #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: 2.73 Å3/Da / Density % sol: 54.88 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 28295 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.211 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE (A CME 94 ) AND RESIDUE (A GLU 95 ) ARE NOT LINKED. DISTANCE OF C-N BOND IS 1.78.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.6001 Å / Origin y: 43.7535 Å / Origin z: 14.8506 Å
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