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- PDB-8bps: Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomi... -

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Basic information

Entry
Database: PDB / ID: 8bps
TitleAspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomium thermophilum CAD-like in apo form
ComponentsCarbamoyl-phosphate synthase (glutamine-hydrolyzing)
KeywordsTRANSFERASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD / cysteine / disulfide bridge / protein stability / crosslinking / succinate / multienzymatic protein
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / aspartate carbamoyltransferase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / hydrolase activity / ATP binding / metal ion binding
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 / 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 / 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 / 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
Uncharacterized protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
Authorsdel Cano-Ochoa, F. / Ramon-Maiques, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTI2018-098084-B-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2021-128468NB-I00 Spain
CitationJournal: Molecules / Year: 2023
Title: A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD.
Authors: Del Cano-Ochoa, F. / Rubio-Del-Campo, A. / Ramon-Maiques, S.
History
DepositionNov 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0487
Polymers35,4951
Non-polymers5536
Water2,234124
1
A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules

A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules

A: Carbamoyl-phosphate synthase (glutamine-hydrolyzing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,14321
Polymers106,4853
Non-polymers1,65818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area10560 Å2
ΔGint-31 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.829, 138.829, 138.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-2306-

GOL

21A-2499-

HOH

31A-2507-

HOH

41A-2511-

HOH

51A-2516-

HOH

61A-2519-

HOH

71A-2522-

HOH

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Components

#1: Protein Carbamoyl-phosphate synthase (glutamine-hydrolyzing)


Mass: 35495.035 Da / Num. of mol.: 1 / Mutation: N2045C, R2238C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0032600 / Plasmid: pOPIN-M-ctATC2Cys / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S583
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: Bipyramidal-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.03→49.08 Å / Num. obs: 325801 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 49.11 Å2 / CC1/2: 1 / Net I/σ(I): 19.9
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 30416 / CC1/2: 0.704 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NNN

5nnn


Resolution: 2.03→49.08 Å / SU ML: 0.2563 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.936
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 1544 5.13 %
Rwork0.1663 28568 -
obs0.1683 30112 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.26 Å2
Refinement stepCycle: LAST / Resolution: 2.03→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 36 124 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052663
X-RAY DIFFRACTIONf_angle_d0.99823622
X-RAY DIFFRACTIONf_chiral_restr0.0501413
X-RAY DIFFRACTIONf_plane_restr0.015469
X-RAY DIFFRACTIONf_dihedral_angle_d7.3316397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.31731320.24172540X-RAY DIFFRACTION100
2.1-2.170.28041500.19252537X-RAY DIFFRACTION100
2.17-2.260.25611280.16282550X-RAY DIFFRACTION100
2.26-2.360.25491240.14442583X-RAY DIFFRACTION99.82
2.36-2.480.19821510.14242547X-RAY DIFFRACTION100
2.48-2.640.19511320.17082551X-RAY DIFFRACTION100
2.64-2.840.24841350.17692592X-RAY DIFFRACTION99.93
2.84-3.130.25931290.17312605X-RAY DIFFRACTION100
3.13-3.580.22891560.16452601X-RAY DIFFRACTION100
3.58-4.510.16171500.13692645X-RAY DIFFRACTION99.86
4.51-100.19051570.1842817X-RAY DIFFRACTION99.6

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