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- PDB-1ml4: The PALA-liganded Aspartate transcarbamoylase catalytic subunit f... -

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Basic information

Entry
Database: PDB / ID: 1ml4
TitleThe PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi
ComponentsAspartate Transcarbamoylase
KeywordsTRANSFERASE / BETA PLEATED SHEET / PROTEIN INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
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 / Rossmann fold ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVan Boxstael, S. / Cunin, R. / Maes, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Aspartate Transcarbamylase from the Hyperthermophilic Archaeon Pyrococcus abyssi: Thermostability and 1.8A Resolution Crystal Structure of the Catalytic Subunit Complexed With the Bisubstrate ...Title: Aspartate Transcarbamylase from the Hyperthermophilic Archaeon Pyrococcus abyssi: Thermostability and 1.8A Resolution Crystal Structure of the Catalytic Subunit Complexed With the Bisubstrate Analogue N-Phosphonacetyl-L-aspartate.
Authors: Van Boxstael, S. / Cunin, R. / Khan, S. / Maes, D.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Aspartate Transcarbamoylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2092
Polymers34,9541
Non-polymers2551
Water1,38777
1
A: Aspartate Transcarbamoylase
hetero molecules

A: Aspartate Transcarbamoylase
hetero molecules

A: Aspartate Transcarbamoylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6286
Polymers104,8633
Non-polymers7653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Aspartate Transcarbamoylase
hetero molecules

A: Aspartate Transcarbamoylase
hetero molecules

A: Aspartate Transcarbamoylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6286
Polymers104,8633
Non-polymers7653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.095, 81.095, 141.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-404-

HOH

DetailsThe biological assembly is a trimer generated by the operations : -Y,X-Y,Z and -X+Y,-X,Z

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Components

#1: Protein Aspartate Transcarbamoylase / Aspartate carbamoyltransferase


Mass: 34954.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PyrB / Plasmid: Ptrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): C600ATC- / References: UniProt: P77918, aspartate carbamoyltransferase
#2: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 50.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: citric acid, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
220 mMTris-HCl1droppH8.2
32 mMbeta-mercaptoethanol1drop
4300 mM1dropNaCl
51.4 Mcitrate1reservoirpH6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 24, 2001
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 29667 / Num. obs: 29667 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.38 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 10.69
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.91 / Num. unique all: 2958 / Rsym value: 0.33 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 70669 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 93 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1EKX

1ekx


Resolution: 1.8→25 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS VERSION FOR HEMIHEDRAL TWINNED DATA
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2651 -RANDOM
Rwork0.172 ---
all0.176 28560 --
obs0.176 28560 88.6 %-
Displacement parametersBiso mean: 27.45 Å2
Baniso -1Baniso -2Baniso -3
1--4.639 Å2-3.45 Å20 Å2
2---4.639 Å20 Å2
3---9.279 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 16 77 2543
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.0961.5
X-RAY DIFFRACTIONc_mcangle_it1.7842
X-RAY DIFFRACTIONc_scbond_it1.7412
X-RAY DIFFRACTIONc_scangle_it2.5562.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.8-1.860.28162510.2924X-RAY DIFFRACTION278687.6
1.86-1.940.28672880.2586X-RAY DIFFRACTION289989.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.2118 / Rfactor Rwork: 0.1718
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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