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Yorodumi- PDB-5dou: Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dou | ||||||||||||
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Title | Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form | ||||||||||||
Components | Carbamoyl-phosphate synthase [ammonia], mitochondrial | ||||||||||||
Keywords | LIGASE / Carbamoyl Phosphate Synthase (ammonia utilizing) / Carbamoyl Phosphate / Ammonia / N-acetyl-L-glutamate / Adenosine Triphosphate / ligand-bound / urea cycle / Multi-domain / Allosteric site / Rare disease / CPS1 deficiency / Hyperammonemia | ||||||||||||
Function / homology | Function and homology information carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / triglyceride catabolic process / modified amino acid binding / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / cellular response to ammonium ion ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / triglyceride catabolic process / modified amino acid binding / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / cellular response to fibroblast growth factor stimulus / response to growth hormone / response to food / glutamate binding / midgut development / nitric oxide metabolic process / response to zinc ion / glutamine metabolic process / response to dexamethasone / cellular response to glucagon stimulus / response to starvation / mitochondrial nucleoid / response to amine / small molecule binding / potassium ion binding / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / response to toxic substance / phospholipid binding / vasodilation / endopeptidase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | de Cima, S. / Polo, L.M. / Fita, I. / Rubio, V. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Sci Rep / Year: 2015 Title: Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. Authors: de Cima, S. / Polo, L.M. / Diez-Fernandez, C. / Martinez, A.I. / Cervera, J. / Fita, I. / Rubio, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dou.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5dou.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 5dou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/5dou ftp://data.pdbj.org/pub/pdb/validation_reports/do/5dou | HTTPS FTP |
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-Related structure data
Related structure data | 5dotSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 43 - 1493 / Label seq-ID: 32 - 1482
NCS ensembles :
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Details | The biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D) |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 164061.797 Da / Num. of mol.: 4 / Fragment: mature enzyme Source method: isolated from a genetically manipulated source Details: Mature CPS1 with N-terminal His-tag for purification purposes Source: (gene. exp.) Homo sapiens (human) / Gene: CPS1 / Organ: LIVER / Plasmid: pFastBac-bMON14272 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P31327, carbamoyl-phosphate synthase (ammonia) |
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-Non-polymers , 10 types, 696 molecules
#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-ADP / #7: Chemical | ChemComp-NLG / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-EDO / | #11: 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: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.4 M MgCl2, 0.2 M ammonium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→40 Å / Num. all: 178654 / Num. obs: 178654 / % possible obs: 90.7 % / Redundancy: 1.8 % / Rpim(I) all: 0.076 / Rrim(I) all: 0.111 / Rsym value: 0.081 / Net I/av σ(I): 7.98 / Net I/σ(I): 7.9 / Num. measured all: 329157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DOT Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2244 / WRfactor Rwork: 0.1917 / FOM work R set: 0.8393 / SU B: 22.763 / SU ML: 0.232 / SU R Cruickshank DPI: 0.2867 / SU Rfree: 0.3226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.323 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.26 Å2 / Biso mean: 45.659 Å2 / Biso min: 2.58 Å2
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Refinement step | Cycle: final / Resolution: 2.6→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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