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Yorodumi- PDB-2vwt: Crystal structure of YfaU, a metal ion dependent class II aldolas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vwt | |||||||||
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Title | Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex | |||||||||
Components | YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE | |||||||||
Keywords | LYASE / (BETA/ALPHA)8 BARREL / 2-KETO-3-DEOXY SUGAR ALDOLASE / ESCHERICHIA COLI K-12 PROTEIN YFAU / DEGRADATION OF HOMOPROTOCATECHUATE / PYRUVATE / CLASS II ALDOLASE | |||||||||
Function / homology | Function and homology information 2-keto-3-deoxy-L-rhamnonate aldolase / 2-keto-3-deoxy-L-rhamnonate aldolase activity / aldehyde-lyase activity / protein hexamerization / nickel cation binding / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å | |||||||||
Authors | Rea, D. / Rakus, J.F. / Gerlt, J.A. / Fulop, V. / Bugg, T.D.H. / Roper, D.I. | |||||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal Structure and Functional Assignment of Yfau, a Metal Ion Dependent Class II Aldolase from Escherichia Coli K12. Authors: Rea, D. / Hovington, R. / Rakus, J.F. / Gerlt, J.A. / Fulop, V. / Bugg, T.D.H. / Roper, D.I. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vwt.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwt.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwt ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwt | HTTPS FTP |
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-Related structure data
Related structure data | 2vwsC 1dxeS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 28942.945 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PT7-7-YFAU / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) References: UniProt: P76469, 2-dehydro-3-deoxyglucarate aldolase |
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-Non-polymers , 5 types, 553 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.5 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE ...Details: WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE HOMOLOGUE FROM ESCHERICHIA COLI K12. ACTA CRYST. D58, 2191-2193., pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→53 Å / Num. obs: 63843 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1DXE Resolution: 1.93→52.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.91 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→52.7 Å
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Refine LS restraints |
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