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- PDB-2vhi: Crystal structure of a pyrimidine degrading enzyme from Drosophil... -

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Basic information

Entry
Database: PDB / ID: 2vhi
TitleCrystal structure of a pyrimidine degrading enzyme from Drosophila melanogaster
ComponentsCG3027-PA
KeywordsHYDROLASE
Function / homology
Function and homology information


Pyrimidine catabolism / beta-ureidopropionase / pyrimidine nucleobase catabolic process / N-carbamoylputrescine amidase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / putrescine biosynthetic process from arginine / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-alanine synthase
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLundgren, S. / Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Crystal Structure of Beta-Alanine Synthase from Drosophila Melanogaster Reveals a Homooctameric Helical Turn-Like Assembly.
Authors: Lundgren, S. / Lohkamp, B. / Andersen, B. / Piskur, J. / Dobritzsch, D.
History
DepositionNov 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG3027-PA
B: CG3027-PA
C: CG3027-PA
D: CG3027-PA
E: CG3027-PA
F: CG3027-PA
G: CG3027-PA
H: CG3027-PA


Theoretical massNumber of molelcules
Total (without water)369,0008
Polymers369,0008
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46930 Å2
ΔGint-467.4 kcal/mol
Surface area120310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)278.863, 95.048, 199.312
Angle α, β, γ (deg.)90.00, 125.82, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31D
41E
51F
61G
12B
22A
32H

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUTHRTHRBB9 - 3869 - 386
211LEULEUTHRTHRCC9 - 3869 - 386
311LEULEUTHRTHRDD9 - 3869 - 386
411LEULEUTHRTHREE9 - 3869 - 386
511LEULEUTHRTHRFF9 - 3869 - 386
611LEULEUTHRTHRGG9 - 3869 - 386
112LEULEUPHEPHEBB9 - 1269 - 126
212LEULEUPHEPHEAA9 - 1269 - 126
312LEULEUPHEPHEHH9 - 1269 - 126
122ALAALAILEILEBB140 - 200140 - 200
222ALAALAILEILEAA140 - 200140 - 200
322ALAALAILEILEHH140 - 200140 - 200
132GLYGLYGLUGLUBB215 - 293215 - 293
232GLYGLYGLUGLUAA215 - 293215 - 293
332GLYGLYGLUGLUHH215 - 293215 - 293
142TYRTYRTHRTHRBB315 - 386315 - 386
242TYRTYRTHRTHRAA315 - 386315 - 386
342TYRTYRTHRTHRHH315 - 386315 - 386

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.7424, -0.19083, -0.64221), (-0.1941, -0.97873, 0.06646), (-0.64123, 0.07531, -0.76364)45.31232, 28.39185, 114.70859
2given(0.13801, -0.03116, -0.98994), (0.16118, 0.98689, -0.0086), (0.97723, -0.15837, 0.14122)92.47089, 6.27514, -11.20712
3given(-0.55374, -0.11704, -0.82442), (-0.11379, -0.97015, 0.21416), (-0.82488, 0.2124, 0.52389)119.88699, 3.21178, 64.56676
4given(-0.95765, 0.11604, -0.26352), (0.1661, 0.9702, -0.17641), (0.23519, -0.21271, -0.94839)115.99371, 27.85579, 76.62392
5given(-0.89473, 0.03218, 0.44544), (0.04237, -0.98679, 0.15639), (0.44459, 0.1588, 0.88155)77.02422, -16.18002, -16.11687
6given(-0.37574, 0.19146, 0.90673), (-0.00178, 0.97828, -0.2073), (-0.92672, -0.07951, -0.36724)32.20789, 52.12144, 108.62991
7given(0.31269, 0.00146, 0.94985), (0.00105, -1, 0.00119), (0.94985, 0.00063, -0.31269)-10.4352, -20.97723, 14.2562

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Components

#1: Protein
CG3027-PA / BETA-ALANINE SYNTHASE


Mass: 46124.949 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VI04, beta-ureidopropionase

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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: 2.97 Å3/Da / Density % sol: 58.68 % / Description: NONE
Crystal growpH: 4.2 / Details: PEG 3350, PHOSPHATE/CITRATE PH 4.2, NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 54793 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.804 / SU B: 27.524 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.673 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2764 5.1 %RANDOM
Rwork0.226 ---
obs0.229 51958 85.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.37 Å2
Baniso -1Baniso -2Baniso -3
1-4.01 Å20 Å22.58 Å2
2--0.48 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23681 0 0 0 23681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02224253
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.94332815
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91452957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90224.0131186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.024154179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.40515172
X-RAY DIFFRACTIONr_chiral_restr0.090.23499
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218645
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.211133
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.216259
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2740
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B1512tight positional0.040.05
12C1512tight positional0.030.05
13D1512tight positional0.040.05
14E1512tight positional0.040.05
15F1512tight positional0.030.05
16G1512tight positional0.030.05
21B1316tight positional0.050.05
22A1316tight positional0.040.05
23H1316tight positional0.040.05
11B1507medium positional0.420.5
12C1507medium positional0.430.5
13D1507medium positional0.420.5
14E1507medium positional0.450.5
15F1507medium positional0.410.5
16G1507medium positional0.420.5
21B1292medium positional0.460.5
22A1292medium positional0.430.5
23H1292medium positional0.40.5
11B1512tight thermal0.070.5
12C1512tight thermal0.040.5
13D1512tight thermal0.040.5
14E1512tight thermal0.050.5
15F1512tight thermal0.040.5
16G1512tight thermal0.050.5
21B1316tight thermal0.10.5
22A1316tight thermal0.060.5
23H1316tight thermal0.060.5
11B1507medium thermal0.392
12C1507medium thermal0.32
13D1507medium thermal0.322
14E1507medium thermal0.342
15F1507medium thermal0.322
16G1507medium thermal0.352
21B1292medium thermal0.452
22A1292medium thermal0.292
23H1292medium thermal0.352
LS refinement shellResolution: 3.3→3.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 187 -
Rwork0.27 3592 -
obs--81.01 %

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