+Open data
-Basic information
Entry | Database: PDB / ID: 1obd | ||||||
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Title | SAICAR-synthase complexed with ATP | ||||||
Components | PHOSPHORIBOSYLAMIDOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE | ||||||
Keywords | LIGASE / SYNTHETASE / ATP BINDING PROTEIN / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYNTHASE / PURINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Urusova, D.V. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K. | ||||||
Citation | Journal: Kristallografiya / Year: 2001 Title: X-Ray Structure of Saicar-Synthase Complexed with ATP Authors: Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Urusova, D.V. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K. #1: Journal: Structure / Year: 1998 Title: The Structure of Saicar Synthase: An Enzyme in the De Novo Pathway of Purine Nucleotide Biosynthesis Authors: Levdikov, V.M. / Barynin, V.V. / Grebenko, A.I. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1obd.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1obd.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 1obd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1obd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1obd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1obd_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 1obd_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/1obd ftp://data.pdbj.org/pub/pdb/validation_reports/ob/1obd | HTTPS FTP |
-Related structure data
Related structure data | 1obgC 1a48S S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34545.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) References: UniProt: P27616, phosphoribosylaminoimidazolesuccinocarboxamide synthase |
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-Non-polymers , 5 types, 532 molecules
#2: Chemical | ChemComp-ATP / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-AMP / | #6: 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: 2.2 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: THE HANGING DROPS CONTAINED PROTEIN AT A CONCENTRATION OF 8 - 15 MG/ML, 50 MM TRIS-HCL BUFFER, PH 7.0, 40 MM ASPARTIC ACID AND 1.0 - 1.25 M AMMONIUM SULPHATE. THE WELL CONTAINED THE SAME ...Details: THE HANGING DROPS CONTAINED PROTEIN AT A CONCENTRATION OF 8 - 15 MG/ML, 50 MM TRIS-HCL BUFFER, PH 7.0, 40 MM ASPARTIC ACID AND 1.0 - 1.25 M AMMONIUM SULPHATE. THE WELL CONTAINED THE SAME ABOVE BUFFER PLUS 2.25 M AMMONIUM SULPHATE |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.906 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.906 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 59985 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7 / % possible all: 97.4 |
Reflection shell | *PLUS % possible obs: 97.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A48 Resolution: 1.4→30 Å / SU B: 0.775 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 15.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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