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- PDB-4ekn: Structure of the catalytic chain of Methanococcus jannaschii Aspa... -

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Basic information

Entry
Database: PDB / ID: 4ekn
TitleStructure of the catalytic chain of Methanococcus jannaschii Aspartate Transcarbamoylase in a hexagonal crystal form
ComponentsAspartate carbamoyltransferase
KeywordsTRANSFERASE / ATCase / aspartate transcarbamoylase / pyrimidine biosynthesis / thermostability / substrate channeling
Function / homology
Function and homology information


aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
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
: / Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4996 Å
AuthorsVitali, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme.
Authors: Vitali, J. / Singh, A.K. / Soares, A.S. / Colaneri, M.J.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
B: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7267
Polymers35,2111
Non-polymers5156
Water2,612145
1
B: Aspartate carbamoyltransferase
hetero molecules

B: Aspartate carbamoyltransferase
hetero molecules

B: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,17821
Polymers105,6323
Non-polymers1,54618
Water543
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
Buried area7850 Å2
ΔGint-154 kcal/mol
Surface area35960 Å2
MethodPISA
2
B: Aspartate carbamoyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)214,35642
Polymers211,2646
Non-polymers3,09336
Water1086
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 area21570 Å2
ΔGint-344 kcal/mol
Surface area66500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.960, 96.960, 136.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-401-

SO4

21B-401-

SO4

31B-403-

SO4

41B-405-

K

51B-406-

GOL

61B-514-

HOH

71B-570-

HOH

81B-643-

HOH

DetailsTrimer. A hexamer is also formed by pisa prediction but it is not known if it has biological relevance

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Components

#1: Protein Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


Mass: 35210.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Description: pSJS1240 was also cotransformed / Gene: MJ1581, pyrB / Plasmid: pEK406 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1594 / References: UniProt: Q58976, aspartate carbamoyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, and 0.1 M Tris-HCl pH 7.5. The protein was a mixture of catalytic and regulatory subunits at a molar ratio of 1:1 ...Details: 2.0 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, and 0.1 M Tris-HCl pH 7.5. The protein was a mixture of catalytic and regulatory subunits at a molar ratio of 1:1 concentrated to 11 mg/ml. Drops consisted of 2ul reservoir and 2.6 ul complex solution., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2010
RadiationMonochromator: Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4996→50 Å / Num. obs: 13471 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.3
Reflection shellResolution: 2.4996→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.62 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY of 2RGW chain D

2rgw


Resolution: 2.4996→41.985 Å / SU ML: 0.35 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1377 10.22 %random
Rwork0.1833 ---
obs0.1922 13469 98.18 %-
all-13471 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.097 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.2243 Å2-0 Å2-0 Å2
2--2.2243 Å2-0 Å2
3----4.4487 Å2
Refinement stepCycle: LAST / Resolution: 2.4996→41.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 27 145 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052529
X-RAY DIFFRACTIONf_angle_d0.6523397
X-RAY DIFFRACTIONf_dihedral_angle_d13.87984
X-RAY DIFFRACTIONf_chiral_restr0.047381
X-RAY DIFFRACTIONf_plane_restr0.002428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.4996-2.5890.31021260.237111870.0276131399
2.589-2.69260.38191440.24511910.0318133599
2.6926-2.81510.34121240.232611980.03061322100
2.8151-2.96350.29531510.213711800.024133199
2.9635-3.14910.30931370.198512000.0264133799
3.1491-3.39220.28561460.190711930.0236133999
3.3922-3.73340.26581260.166612340.0237136099
3.7334-4.27310.23791480.145212080.0196135699
4.2731-5.38190.20921270.141712440.0186137197
5.3819-41.99080.24961480.19612570.0205140592

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