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- PDB-3d6n: Crystal Structure of Aquifex Dihydroorotase Activated by Aspartat... -

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Basic information

Entry
Database: PDB / ID: 3d6n
TitleCrystal Structure of Aquifex Dihydroorotase Activated by Aspartate Transcarbamoylase
Components
  • Aspartate carbamoyltransferase
  • Dihydroorotase
KeywordsHYDROLASE/TRANSFERASE / REACTOR / CHAMBER / PORES / INTERNAL CAVITY / Hydrolase / Metal-binding / Pyrimidine biosynthesis / Transferase / HYDROLASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


allantoinase activity / dihydroorotase / purine nucleobase catabolic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...allantoinase activity / dihydroorotase / purine nucleobase catabolic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 ...Dihydroorotase / : / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / 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 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Aspartate carbamoyltransferase catalytic subunit / Dihydroorotase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsEdwards, B.F.P.
CitationJournal: Biochemistry / Year: 2009
Title: Dihydroorotase from the hyperthermophile Aquifiex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.
Authors: Zhang, P. / Martin, P.D. / Purcarea, C. / Vaishnav, A. / Brunzelle, J.S. / Fernando, R. / Guy-Evans, H.I. / Evans, D.R. / Edwards, B.F.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotase
B: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4915
Polymers80,0472
Non-polymers4443
Water7,602422
1
A: Dihydroorotase
B: Aspartate carbamoyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)482,94530
Polymers480,28412
Non-polymers2,66218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area46140 Å2
ΔGint-384 kcal/mol
Surface area137360 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-49 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.439, 158.439, 233.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21B-419-

HOH

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Components

#1: Protein Dihydroorotase / DHOase


Mass: 46440.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: pyrC, aq_806 / Plasmid: pAApyrC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66990, dihydroorotase
#2: Protein Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


Mass: 33606.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: pyrB, aq_409 / Plasmid: pAApyrB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66726, aspartate carbamoyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3 mg/mL protein in 10mM Hepes, 10 mM sodium citrate, 2 mM DTT mixed 6:1 with 25% ethylene glycol, 10mM BaCL2 and equilibrated with same., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2006
RadiationMonochromator: Si(111) double-crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→65 Å / Num. all: 47628 / Num. obs: 47614 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 34.4 Å2 / Rsym value: 0.8 / Net I/σ(I): 23.83
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.96 / Num. unique all: 9768 / Rsym value: 0.546 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD
Starting model: 1xrtA, 1ml4

1ml4


Resolution: 2.3→65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.642 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20404 2544 5.1 %RANDOM
Rwork0.16444 ---
all0.1665 47628 --
obs0.16646 47614 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.171 Å0.197 Å
Luzzati sigma a-0.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 27 422 6081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225765
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9817784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9845711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41624.413247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.876151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9331532
X-RAY DIFFRACTIONr_chiral_restr0.1320.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024264
X-RAY DIFFRACTIONr_nbd_refined0.2130.22692
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2397
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.234
X-RAY DIFFRACTIONr_mcbond_it1.0691.53678
X-RAY DIFFRACTIONr_mcangle_it1.66525765
X-RAY DIFFRACTIONr_scbond_it2.92632367
X-RAY DIFFRACTIONr_scangle_it4.5024.52019
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 184 -
Rwork0.185 3500 -
obs-3500 100 %
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)
10.8327-0.37110.16371.2812-0.02761.30410.0130.10590.2334-0.1888-0.0261-0.3575-0.14420.39970.0131-0.0931-0.11370.06030.05120.03220.00340.12722.55107.915
265.5776-60.999276.2643109.2158-119.1642133.0105-0.6019-3.6176-0.2939-1.92030.01431.7212-3.5043-1.44660.58760.08670.0311-0.01860.0506-0.01310.066329.67317.561104.663
30.6305-0.4028-0.12471.63490.57070.8437-0.02160.07250.0598-0.0632-0.0055-0.0367-0.05950.04050.0271-0.0264-0.02210.0203-0.08660.074-0.10364.23722.84679.759
498.3952-90.857111.710988.3364-3.780612.53450.6397-1.7861-1.05440.97620.18775.9451-0.695-4.13-0.82740.05480.0345-0.00550.04050.00980.03341.66819.80984.687
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4221 - 422
2X-RAY DIFFRACTION2AD4241
3X-RAY DIFFRACTION3BB1 - 2911 - 291
4X-RAY DIFFRACTION4BE2921

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