+Open data
-Basic information
Entry | Database: PDB / ID: 1gvf | ||||||
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Title | Structure of tagatose-1,6-bisphosphate aldolase | ||||||
Components | TAGATOSE-BISPHOSPHATE ALDOLASE AGAY | ||||||
Keywords | LYASE / ZINC. | ||||||
Function / homology | Function and homology information tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / D-tagatose 6-phosphate catabolic process / carbohydrate metabolic process / protein-containing complex / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.45 Å | ||||||
Authors | Hall, D.R. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of Tagatose-1,6-Bisphosphate Aldolase; Insight Into Chiral Discrimination, Mechanism and Specificity of Class II Aldolases Authors: Hall, D.R. / Bond, C.S. / Leonard, G.A. / Watt, C.I. / Berry, A. / Hunter, W.N. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY A 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 1gvf.cif.gz | 255.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gvf.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 1gvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gvf_validation.pdf.gz | 424.5 KB | Display | wwPDB validaton report |
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Full document | 1gvf_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 1gvf_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1gvf_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvf ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvf | 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.02797, -0.99947, -0.01649), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31330.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P42908, UniProt: P0AB74*PLUS, tagatose-bisphosphate aldolase |
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-Non-polymers , 5 types, 678 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THE ASYMMETRIC UNIT CONTAINS A DIMER WHICH BY MEANS OF A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY ...THE ASYMMETRIC |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.7 % Description: WAVELENGTHS QUOTED ARE FOR MAD PEAK, MAD INFLECTION POINT, MAD REMOTE 1, MAD REMOTE2, INHOUSE REFINEMENT, ID14-EH2 HIGH RES REFINEMENT DATA SETS RESPECTIVELY EXPERIMENTAL STATISTICS ...Description: WAVELENGTHS QUOTED ARE FOR MAD PEAK, MAD INFLECTION POINT, MAD REMOTE 1, MAD REMOTE2, INHOUSE REFINEMENT, ID14-EH2 HIGH RES REFINEMENT DATA SETS RESPECTIVELY EXPERIMENTAL STATISTICS QUOTED FOR COMBINED INHOUSE AND HIGH RES DATA SET USED FOR REFINEMENT | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.40 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ESRF / Beamline: BM14 / Wavelength: 1.282,1.283,1.127,1.030, 1.5418,0.933 | |||||||||||||||||||||
Detector | Type: MAR, RAXIS / Detector: CCD | |||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.45→29.8 Å / Num. obs: 1086028 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15 | |||||||||||||||||||||
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 1.5 / % possible all: 97.9 | |||||||||||||||||||||
Reflection | *PLUS Num. obs: 131455 / Num. measured all: 1086028 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.45→10 Å / Num. parameters: 47082 / Num. restraintsaints: 56585 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ARP/WARP WITH REFMAC USED FIRST FOLLOWED BY CNS THE FOLLOWING RESIDUES HAVE MISSING ATOMS DUE TO DISORDER: SER A 151 LYS A 185 LYS A 188 ARG A 257 SER A 285 GLU B 150 SER B 151 LYS B 185 LYS B 188 GLU B 216
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 15 / Occupancy sum hydrogen: 4167 / Occupancy sum non hydrogen: 4926.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor all: 0.13 / Rfactor obs: 0.17 / Rfactor Rfree: 0.13 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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