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- PDB-6hfi: Human dihydroorotase mutant F1563A apo structure -

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Basic information

Entry
Database: PDB / ID: 6hfi
TitleHuman dihydroorotase mutant F1563A apo structure
ComponentsCAD protein
KeywordsBIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine
Function / homology
Function and homology information


aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / glutaminase activity / UTP biosynthetic process / response to caffeine / glutamine metabolic process / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / animal organ regeneration / lactation / cellular response to epidermal growth factor stimulus / xenobiotic metabolic process / liver development / cell projection / female pregnancy / peptidyl-threonine phosphorylation / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
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 / Glutamine amidotransferase / Aspartate/ornithine carbamoyltransferase superfamily / Glutamine amidotransferase class-I / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / 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 / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45994719309 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_alt_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)43,33210
Polymers42,8401
Non-polymers4929
Water6,936385
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,66320
Polymers85,6802
Non-polymers98418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5040 Å2
ΔGint-320 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.800, 159.090, 61.300
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-1905-

FMT

21A-1905-

FMT

31A-2323-

HOH

41A-2343-

HOH

51A-2352-

HOH

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Components

#1: Protein CAD protein


Mass: 42839.922 Da / Num. of mol.: 1 / Mutation: F1563A
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-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
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 Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45994719309→79.5 Å / Num. obs: 132840 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.7407121106 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1.45994719309→1.5 Å / Redundancy: 3.1 % / Num. unique obs: 5050 / CC1/2: 0.901 / Rrim(I) all: 0.714 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c6c

4c6c


Resolution: 1.45994719309→28.2453922211 Å / SU ML: 0.123061189221 / Cross valid method: FREE R-VALUE / σ(F): 0.99157497576 / Phase error: 15.0848033216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.164081947133 6646 5.00301114122 %
Rwork0.128309415983 126194 -
obs0.130072421259 132840 98.969625176 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.808431408 Å2
Refinement stepCycle: LAST / Resolution: 1.45994719309→28.2453922211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 19 389 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01336559887593004
X-RAY DIFFRACTIONf_angle_d1.302159125814116
X-RAY DIFFRACTIONf_chiral_restr0.224739614964461
X-RAY DIFFRACTIONf_plane_restr0.00888228152829546
X-RAY DIFFRACTIONf_dihedral_angle_d26.15543223251134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4599-1.47650.3155731804342150.2857131179624079X-RAY DIFFRACTION96.9081471451
1.4765-1.49390.2648248892442200.2516799486194223X-RAY DIFFRACTION99.3515205725
1.4939-1.51210.2151281934162240.1852486558774239X-RAY DIFFRACTION99.5538701762
1.5121-1.53130.1928232801722210.172713834664204X-RAY DIFFRACTION99.0597716588
1.5313-1.55140.2118933506982200.1674447415294287X-RAY DIFFRACTION99.7344545253
1.5514-1.57270.2094773832182220.1587970801994255X-RAY DIFFRACTION99.710467706
1.5727-1.59510.1913361604592200.1460533147474201X-RAY DIFFRACTION99.8419150858
1.5951-1.61890.178877167852260.1439551800714270X-RAY DIFFRACTION99.8002219756
1.6189-1.64420.1675124944312260.1421612691434203X-RAY DIFFRACTION99.8422001803
1.6442-1.67120.1869697301162220.1293012454674240X-RAY DIFFRACTION99.8657117278
1.6712-1.70.1591375061112240.1199556200674273X-RAY DIFFRACTION99.9555456768
1.7-1.73090.1592654842812220.1180745733084209X-RAY DIFFRACTION99.7523638001
1.7309-1.76420.1530379353792230.1106450995924276X-RAY DIFFRACTION99.9777777778
1.7642-1.80020.1623271392052240.1088391612014257X-RAY DIFFRACTION99.9330954505
1.8002-1.83930.1517477028752230.1026576905764209X-RAY DIFFRACTION99.8873112463
1.8393-1.88210.1308760313992240.1060660932974210X-RAY DIFFRACTION99.5509654243
1.8821-1.92920.2366015306982070.1732602587143929X-RAY DIFFRACTION91.2621359223
1.9292-1.98130.1573666687112180.1246882560424184X-RAY DIFFRACTION98.324771052
1.9813-2.03960.1392677345812220.1157663328664254X-RAY DIFFRACTION99.7326203209
2.0396-2.10540.1716106047632210.105978029334188X-RAY DIFFRACTION99.2570914003
2.1054-2.18060.1530175448942230.102802724434261X-RAY DIFFRACTION99.8663697105
2.1806-2.26790.2051866750062140.1300322266293963X-RAY DIFFRACTION93.0289532294
2.2679-2.37110.1440527297752200.112923026564215X-RAY DIFFRACTION99.6405302179
2.3711-2.4960.1292954976822200.1042809076464221X-RAY DIFFRACTION99.5963220453
2.496-2.65230.1523499875862280.1134072268034249X-RAY DIFFRACTION99.5995550612
2.6523-2.85690.1646101758452110.1281279689094221X-RAY DIFFRACTION99.595505618
2.8569-3.14410.1793615965762250.1312026895624241X-RAY DIFFRACTION99.7320232247
3.1441-3.59820.1506409652352300.1227561372834256X-RAY DIFFRACTION99.4899090707
3.5982-4.53040.1373241004322230.1149033395494156X-RAY DIFFRACTION98.2279048901
4.5304-28.25070.167639402932280.1539994126544221X-RAY DIFFRACTION99.1973244147

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