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- PDB-5g1p: Aspartate transcarbamoylase domain of human CAD bound to carbamoy... -

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Basic information

Entry
Database: PDB / ID: 5g1p
TitleAspartate transcarbamoylase domain of human CAD bound to carbamoyl phosphate
ComponentsCAD PROTEIN
KeywordsTRANSFERASE / DE NOVO PYRIMIDINE SYNTHESIS / TRANSCARBAMOYLASE / TRANSCARBAMYLASE / CAD / CARBAMOYL PHOSPHATE SYNTHETASE / DIHYDROOROTASE / COOPERATIVITY
Function / homology
Function and homology information


aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / response to cortisol / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity ...aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / response to cortisol / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutaminase / dihydroorotase activity / Pyrimidine biosynthesis / glutaminase activity / UDP biosynthetic process / glutamine metabolic process / UTP biosynthetic process / response to caffeine / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / cell projection / liver development / female pregnancy / response to insulin / nuclear matrix / terminal bouton / heart development / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Glutamine amidotransferase / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Multifunctional protein CAD
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsRuiz-Ramos, A. / Grande-Garcia, A. / Moreno-Morcillo, M.D. / Ramon-Maiques, S.
Citation
Journal: Structure / Year: 2016
Title: Structure and Functional Characterization of Human Aspartate Transcarbamoylase, the Target of the Anti-Tumoral Drug Pala.
Authors: Ruiz-Ramos, A. / Velazquez-Campoy, A. / Grande-Garcia, A. / Moreno-Morcillo, M. / Ramon-Maiques, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Expression, Purification, Crystallization and Preliminary X- Ray Diffraction Analysis of the Aspartate Transcarbamoylase Domain of Human Cad.
Authors: Ruiz-Ramos, A. / Lallous, N. / Grande-Garcia, A. / Ramon-Maiques, S.
History
DepositionMar 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references / Structure summary
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAD PROTEIN
B: CAD PROTEIN
C: CAD PROTEIN
D: CAD PROTEIN
E: CAD PROTEIN
F: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,31512
Polymers209,4696
Non-polymers8466
Water1,71195
1
D: CAD PROTEIN
E: CAD PROTEIN
F: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1576
Polymers104,7343
Non-polymers4233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-44.7 kcal/mol
Surface area35930 Å2
MethodPISA
2
A: CAD PROTEIN
B: CAD PROTEIN
C: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1576
Polymers104,7343
Non-polymers4233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-43.7 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.670, 157.670, 83.540
Angle α, β, γ (deg.)90.00, 120.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CAD PROTEIN / ASPARTATE TRANSCARBAMOYLASE


Mass: 34911.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN CDNA PURCHASED FROM OPENBIOSYSTEMS (CLONE ID 5551082)
Plasmid: POPIN-M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P27708, aspartate carbamoyltransferase
#2: Chemical
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 0.1 M TRIS PH 8.5, 6% PEG 8000, 11% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.284
11H, -K, -H-L20.225
11L, -K, H30.188
11L, K, -H-L40.119
11-H-L, K, H50.099
11H+L, -K, -L60.085
ReflectionResolution: 3.2→50 Å / Num. obs: 29277 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CSU

3csu


Resolution: 3.19→42.54 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.831 / SU B: 19.999 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25069 1615 5.2 %RANDOM
Rwork0.22067 ---
obs0.22226 29277 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.033 Å2
Baniso -1Baniso -2Baniso -3
1--6.31 Å20 Å2-3.41 Å2
2--32.18 Å20 Å2
3----25.87 Å2
Refinement stepCycle: LAST / Resolution: 3.19→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13050 0 48 95 13193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913303
X-RAY DIFFRACTIONr_bond_other_d0.0080.0213027
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.95818023
X-RAY DIFFRACTIONr_angle_other_deg1.623329777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36951743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35822.667495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.185152158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.22415103
X-RAY DIFFRACTIONr_chiral_restr0.0810.22143
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115016
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6715.1277044
X-RAY DIFFRACTIONr_mcbond_other3.6735.1297031
X-RAY DIFFRACTIONr_mcangle_it6.1117.6878761
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7825.056259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.193→3.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 93 -
Rwork0.232 1985 -
obs--92.11 %

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