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- PDB-6hfs: Human dihydroorotase mutant F1563Y co-crystallized with carbamoyl... -

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Basic information

Entry
Database: PDB / ID: 6hfs
TitleHuman dihydroorotase mutant F1563Y co-crystallized with carbamoyl aspartate at pH 6.5
ComponentsCAD protein
KeywordsBIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine
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 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. / Metal-dependent hydrolases / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / N-CARBAMOYL-L-ASPARTATE / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34904510922 Å
AuthorsRamon-Maiques, S. / Grande Garcia, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-80570-R Spain
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD.
Authors: Del Cano-Ochoa, F. / Grande-Garcia, A. / Reverte-Lopez, M. / D'Abramo, M. / Ramon-Maiques, S.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4949
Polymers42,9181
Non-polymers5768
Water6,413356
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98818
Polymers85,8362
Non-polymers1,15216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5170 Å2
ΔGint-338 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.697, 159.029, 60.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1908-

FMT

21A-1908-

FMT

31A-2313-

HOH

41A-2327-

HOH

51A-2336-

HOH

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Components

#1: Protein CAD protein


Mass: 42917.992 Da / Num. of mol.: 1 / Mutation: F1563Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M / Cell line (production host): HEK293 GnTI / Production host: Homo sapiens (human)
References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP with 4 mM carbamoyl asparate. Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34904510922→40.8485 Å / Num. obs: 87210 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.4913051615 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.045 / Net I/σ(I): 19.9
Reflection shellResolution: 1.34904510922→1.4 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8559 / CC1/2: 0.892 / Rrim(I) all: 0.704 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6I

4c6i


Resolution: 1.34904510922→40.8485 Å / SU ML: 0.0988820373565 / Cross valid method: FREE R-VALUE / σ(F): 1.33793366533 / Phase error: 13.9277847375
RfactorNum. reflection% reflection
Rfree0.145818041585 4315 4.95043825433 %
Rwork0.12525503624 --
obs0.126225775089 87164 99.7345416266 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.1320264029 Å2
Refinement stepCycle: LAST / Resolution: 1.34904510922→40.8485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 25 361 3175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009949468910873025
X-RAY DIFFRACTIONf_angle_d1.14073895554149
X-RAY DIFFRACTIONf_chiral_restr0.158780627359464
X-RAY DIFFRACTIONf_plane_restr0.00816611709207554
X-RAY DIFFRACTIONf_dihedral_angle_d24.78454822621133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.349-1.36440.2582827576121530.212756118972603X-RAY DIFFRACTION96.3299545613
1.3644-1.38040.2176628326281380.207737295932761X-RAY DIFFRACTION99.8966230186
1.3804-1.39730.2202590998921560.1847628706472734X-RAY DIFFRACTION99.6208204068
1.3973-1.4150.2225362610781510.1819187463852704X-RAY DIFFRACTION99.7902831178
1.415-1.43360.1819088070471710.1695538638662704X-RAY DIFFRACTION99.8263888889
1.4336-1.45320.1937692462581750.160678358452747X-RAY DIFFRACTION99.9657885734
1.4532-1.4740.181863354611340.1511939721482698X-RAY DIFFRACTION99.7885835095
1.474-1.4960.1645430095921540.1411415730442749X-RAY DIFFRACTION99.622512011
1.496-1.51940.1584406388271340.1290468618382755X-RAY DIFFRACTION99.792746114
1.5194-1.54430.161109165141470.1221932818232734X-RAY DIFFRACTION99.9306278182
1.5443-1.57090.140854505471240.1185229460692779X-RAY DIFFRACTION100
1.5709-1.59950.1319068940371410.1153213865562731X-RAY DIFFRACTION99.9651931779
1.5995-1.63020.1492465205361240.1120198506262753X-RAY DIFFRACTION99.9305314345
1.6302-1.66350.1475078642331390.1097410347492771X-RAY DIFFRACTION99.9313186813
1.6635-1.69970.1253688005161420.1097656506712749X-RAY DIFFRACTION100
1.6997-1.73920.1450951865631490.1084245097582751X-RAY DIFFRACTION99.9310820124
1.7392-1.78270.1346142316011720.1058951903462725X-RAY DIFFRACTION99.9654934438
1.7827-1.83090.1484369196581350.1090257147282755X-RAY DIFFRACTION99.8617829993
1.8309-1.88480.1413193533481620.1097725085262728X-RAY DIFFRACTION99.72394755
1.8848-1.94560.128429299561360.1105065551842771X-RAY DIFFRACTION99.9312478515
1.9456-2.01510.1309366488921300.1089322985892779X-RAY DIFFRACTION100
2.0151-2.09580.1433123768741300.1060347010442786X-RAY DIFFRACTION99.931459904
2.0958-2.19120.1242859135041540.1026924290692763X-RAY DIFFRACTION100
2.1912-2.30670.1270174306631470.1056621839242772X-RAY DIFFRACTION99.9315302978
2.3067-2.45120.1373075665741470.1065611850262787X-RAY DIFFRACTION99.897854954
2.4512-2.64050.1393595729471340.1182495037582806X-RAY DIFFRACTION99.4587280108
2.6405-2.90610.1468505442991270.1306774019722812X-RAY DIFFRACTION100
2.9061-3.32650.1531634909411370.1275373107072816X-RAY DIFFRACTION100
3.3265-4.19030.1330660843131420.119322041322850X-RAY DIFFRACTION99.8331664998
4.1903-40.86720.1571389781831300.1537728414112976X-RAY DIFFRACTION99.2649408757

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