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Yorodumi- PDB-5at1: STRUCTURAL CONSEQUENCES OF EFFECTOR BINDING TO THE T STATE OF ASP... -
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-Basic information
Entry | Database: PDB / ID: 5at1 | |||||||||
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Title | STRUCTURAL CONSEQUENCES OF EFFECTOR BINDING TO THE T STATE OF ASPARTATE CARBAMOYLTRANSFERASE. CRYSTAL STRUCTURES OF THE UNLIGATED AND ATP-, AND CTP-COMPLEXED ENZYMES AT 2.6-ANGSTROMS RESOLUTION | |||||||||
Components |
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Keywords | TRANSFERASE (CARBAMOYL-P / ASPARTATE) | |||||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | |||||||||
Authors | Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N. | |||||||||
Citation | Journal: Biochemistry / Year: 1990 Title: Structural consequences of effector binding to the T state of aspartate carbamoyltransferase: crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-A resolution. Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N. #1: Journal: Biochemistry / Year: 1990 Title: Crystal Structures of Aspartate Carbamoyltransferase Ligated with Phosphonoacetamide, Malonate, and Ctp or ATP at 2.8-Angstroms Resolution and Neutral Ph Authors: Gouaux, J.E. / Stevens, R.C. / Lipscomb, W.N. #2: Journal: Biochemistry / Year: 1990 Title: Crystal Structures of Phosphonoacetamide Ligated T and Phosphonoacetamide and Malonate Ligated R States of Aspartate Carbamoyltransferase at 2.8-Angstroms Resolution and Neutral Ph Authors: Gouaux, J.E. / Lipscomb, W.N. #3: Journal: Biochemistry / Year: 1989 Title: Structure of a Single Amino Acid Mutant of Aspartate Carbamoyltransferase at 2.5-Angstroms Resolution. Implications for the Cooperative Mechanism Authors: Gouaux, J.E. / Lipscomb, W.N. / Middleton, S.A. / Kantrowitz, E.R. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase Authors: Gouaux, J.E. / Lipscomb, W.N. #5: Journal: J.Mol.Biol. / Year: 1988 Title: Complex of N-Phosphonacetyl-L-Aspartate with Aspartate Carbamoyltransferase. X-Ray Refinement, Analysis of Conformational Changes and Catalytic and Allosteric Mechanisms Authors: Ke, H. / Lipscomb, W.N. / Cho, Y. / Honzatko, R.B. #6: Journal: Science / Year: 1988 Title: Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function Authors: Kantrowitz, E.R. / Lipscomb, W.N. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988 Title: Three-Dimensional Structure of Carbamoyl Phosphate and Succinate Bound to Aspartate Carbamoyltransferase Authors: Gouaux, J.E. / Lipscomb, W.N. #8: Journal: J.Mol.Biol. / Year: 1987 Title: Structural Asymmetry in the Ctp-Liganded Form of Aspartate Carbamoyltransferase from Escherichia Coli Authors: Kim, K.H. / Pan, Z. / Honzatko, R.B. / Ke, H. / Lipscomb, W.N. #9: Journal: J.Mol.Biol. / Year: 1987 Title: 2.5 Angstroms Structure of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analog N-(Phosphonacetyl)-L-Aspartate Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N. #10: Journal: Biochem.Biophys.Res.Commun. / Year: 1987 Title: The Catalytic Mechanism of Escherichia Coli Aspartate Carbamoyltransferase. A Molecular Modelling Study Authors: Gouaux, J.E. / Krause, K.L. / Lipscomb, W.N. #11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985 Title: Structure at 2.9-Angstroms Resolution of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analogue N-(Phosphonacetyl)-L-Aspartate Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N. #12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984 Title: Structure of Unligated Aspartate Carbamoyltransferase of Escherichia Coli at 2.6-Angstroms Resolution Authors: Ke, H. / Honzatko, R.B. / Lipscomb, W.N. #13: Journal: J.Mol.Biol. / Year: 1982 Title: Crystal and Molecular Structures of Native and Ctp-Liganded Aspartate Carbamoyltransferase from Escherichia Coli Authors: Honzatko, R.B. / Crawford, J.L. / Monaco, H.L. / Ladner, J.E. / Edwards, B.F.P. / Evans, D.R. / Warren, S.G. / Wiley, D.C. / Ladner, R.C. / Lipscomb, W.N. #14: Journal: J.Mol.Biol. / Year: 1982 Title: Interactions of Phosphate Ligands with Escherichia Coli Aspartate Carbamoyltransferase in the Crystalline State Authors: Honzatko, R.B. / Lipscomb, W.N. #15: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982 Title: Interactions of Metal-Nucleotide Complexes with Aspartate Carbamoyltransferase in the Crystalline State Authors: Honzatko, R.B. / Lipscomb, W.N. #16: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982 Title: Gross Quaternary Changes in Aspartate Carbamoyltransferase are Induced by the Binding of N-(Phosphonacetyl)-L-Aspartate. A 3.5-Angstroms Resolution Study Authors: Ladner, J.E. / Kitchell, J.P. / Honzatko, R.B. / Ke, H.M. / Volz, K.W. / Kalb(Gilboa), A.J. / Ladner, R.C. / Lipscomb, W.N. #17: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979 Title: A 3.0-Angstroms Resolution Study of Nucleotide Complexes with Aspartate Carbamoyltransferase Authors: Honzatko, R.B. / Monaco, H.L. / Lipscomb, W.N. #18: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978 Title: Three-Dimensional Structures of Aspartate Carbamoyltransferase from Escherichia Coli and of its Complex with Cytidine Triphosphate Authors: Monaco, H.L. / Crawford, J.L. / Lipscomb, W.N. #19: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN Year: 1975 Title: Binding Site at 5.5 Angstroms Resolution of Cytidine Triphosphate, the Allosteric Inhibitor of Aspartate Transcarbamylase from Escherichia Coli. Relation to Mechanisms of Control Authors: Lipscomb, W.N. / Edwards, B.F.P. / Evans, D.R. / Pastra-Landis, S.C. #20: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973 Title: Aspartate Transcarbamoylase from Escherichia Coli. Electron Density at 5.5 Angstroms Resolution Authors: Warren, S.G. / Edwards, B.F.P. / Evans, D.R. / Wiley, D.C. / Lipscomb, W.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5at1.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5at1.ent.gz | 153 KB | Display | PDB format |
PDBx/mmJSON format | 5at1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5at1_validation.pdf.gz | 530.6 KB | Display | wwPDB validaton report |
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Full document | 5at1_full_validation.pdf.gz | 566.7 KB | Display | |
Data in XML | 5at1_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 5at1_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/5at1 ftp://data.pdbj.org/pub/pdb/validation_reports/at/5at1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO A 268 AND PRO C 268 ARE CIS-PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.2563, -0.9665, 0.0114), Vector: Details | THE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS, WHICH IS SPECIFIED ON THE *MTRIX* RECORDS BELOW, RELATES THE *A* AND *B* CHAINS TO THE *C* AND *D* CHAINS. | |
-Components
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17072.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7F3 #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.7 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 23334 / Num. measured all: 113912 / Rmerge(I) obs: 0.06 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.6→10 Å / Rfactor Rwork: 0.16 Details: THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T STATE STRUCTURE AGAINST HIGHER ...Details: THE UNUSUAL B VALUES IN THIS COORDINATE SET ARE DISCUSSED IN THE PAPER CITED ON THE *JRNL* RECORDS ABOVE. BASED ON PRELIMINARY REFINEMENT OF ANOTHER T STATE STRUCTURE AGAINST HIGHER RESOLUTION DATA, A MORE TYPICAL B VALUE DISTRIBUTION WAS FOUND. THESE NEW RESULTS WILL BE PUBLISHED WHEN THE REFINEMENT AND ANALYSIS IS COMPLETE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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