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- PDB-1pg5: CRYSTAL STRUCTURE OF THE UNLIGATED (T-STATE) ASPARTATE TRANSCARBA... -

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Basic information

Entry
Database: PDB / ID: 1pg5
TitleCRYSTAL STRUCTURE OF THE UNLIGATED (T-STATE) ASPARTATE TRANSCARBAMOYLASE FROM THE EXTREMELY THERMOPHILIC ARCHAEON SULFOLOBUS ACIDOCALDARIUS
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsTRANSFERASE
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / 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 / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase regulatory chain / Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDe Vos, D. / Van Petegem, F. / Remaut, H. / Legrain, C. / Glansdorff, N. / Van Beeumen, J.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of T State Aspartate Carbamoyltransferase of the Hyperthermophilic Archaeon Sulfolobus acidocaldarius.
Authors: De Vos, D. / Van Petegem, F. / Remaut, H. / Legrain, C. / Glansdorff, N. / Van Beeumen, J.J.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQRES Author states that according to the publication of Durbecq et al. in Eur J Bioch 264, 233- ...SEQRES Author states that according to the publication of Durbecq et al. in Eur J Bioch 264, 233-241 (1999) and according to our crystal structure the correct residue at position 1 of the catalytic chain is a Leu.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1123
Polymers53,0462
Non-polymers651
Water1,67593
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)318,67118
Polymers318,27912
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area24450 Å2
ΔGint-95 kcal/mol
Surface area108970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.853, 132.853, 140.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Aspartate carbamoyltransferase / Aspartate transcarbamylase / Aspartate carbamoyltransferase / ATCase


Mass: 34201.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: PYRB / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55338, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain / Aspartate transcarbamylase / Aspartate carbamoyltransferase


Mass: 18845.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: PYRI / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / References: UniProt: P74766
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulfate, sodium acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→20 Å / Num. all: 23210 / Num. obs: 23141 / % possible obs: 99.7 %
Reflection shellResolution: 2.59→2.64 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8AT1

8at1


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.721 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.23862 1156 5 %RANDOM
Rwork0.19291 ---
all0.19521 ---
obs0.19521 21788 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.444 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 1 93 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223561
X-RAY DIFFRACTIONr_bond_other_d0.0030.023367
X-RAY DIFFRACTIONr_angle_refined_deg2.4521.9764803
X-RAY DIFFRACTIONr_angle_other_deg1.10337859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435437
X-RAY DIFFRACTIONr_chiral_restr0.1370.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023835
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02670
X-RAY DIFFRACTIONr_nbd_refined0.220.2681
X-RAY DIFFRACTIONr_nbd_other0.2470.23793
X-RAY DIFFRACTIONr_nbtor_other0.1030.22306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.24
X-RAY DIFFRACTIONr_mcbond_it1.0671.52196
X-RAY DIFFRACTIONr_mcangle_it2.00323583
X-RAY DIFFRACTIONr_scbond_it3.00131365
X-RAY DIFFRACTIONr_scangle_it5.1324.51220
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 73
Rwork0.239 1547
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2314-0.3553-0.34481.9945-0.10421.20440.06380.0004-0.0679-0.201-0.0276-0.10490.22240.1253-0.03620.11740.0189-0.02180.1093-0.0080.078286.74424.4360.376
22.9705-0.31860.40013.4650.1156.107-0.0648-0.1424-0.0704-0.0472-0.0131-0.2012-0.19150.10490.07790.0272-0.0336-0.0060.16880.01480.0404118.29560.09143.612
39.16442.6011-2.49222.56190.54393.8143-0.02850.0921-0.2553-0.19170.0205-0.33060.01880.29250.0080.0688-0.04360.07110.14980.02450.1222102.59142.80147.582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA100 - 299100 - 299
2X-RAY DIFFRACTION2BB11 - 10215 - 106
3X-RAY DIFFRACTION3BB103 - 160107 - 164

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