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

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Basic information

Entry
Database: PDB / ID: 2vhh
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: 2.8 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


Theoretical massNumber of molelcules
Total (without water)184,5004
Polymers184,5004
Non-polymers00
Water0
1
A: CG3027-PA
B: CG3027-PA
C: CG3027-PA
D: CG3027-PA

A: CG3027-PA
B: CG3027-PA
C: CG3027-PA
D: CG3027-PA


Theoretical massNumber of molelcules
Total (without water)369,0008
Polymers369,0008
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area51230 Å2
ΔGint-514.6 kcal/mol
Surface area123070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)95.040, 197.880, 97.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31D
12C
22A

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
111LEULEUTHRTHRCC9 - 3869 - 386
211LEULEUTHRTHRBB9 - 3869 - 386
311LEULEUTHRTHRDD9 - 3869 - 386
112LEULEUPHEPHECC9 - 1269 - 126
212LEULEUPHEPHEAA9 - 1269 - 126
122ALAALAILEILECC140 - 200140 - 200
222ALAALAILEILEAA140 - 200140 - 200
132GLYGLYGLUGLUCC215 - 293215 - 293
232GLYGLYGLUGLUAA215 - 293215 - 293
142TYRTYRTHRTHRCC315 - 386315 - 386
242TYRTYRTHRTHRAA315 - 386315 - 386

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.98623, 0.13275, 0.09859), (0.14531, 0.41124, 0.89987), (0.07892, 0.90181, -0.42487)-139.90811, -1.75407, 24.16929
2given(0.99119, -0.07714, -0.10763), (-0.09451, 0.15724, -0.98303), (0.09275, 0.98454, 0.14857)-13.95304, 9.88206, 16.84273
3given(-0.98215, 0.18607, -0.0276), (0.18628, 0.94161, -0.28047), (-0.0262, -0.28061, -0.95946)-123.26457, 15.33319, 25.95802

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Components

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


Mass: 46124.949 Da / Num. of mol.: 4
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: 2.56 Å3/Da / Density % sol: 52 % / 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: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 43922 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.877 / SU B: 14.178 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2237 5.1 %RANDOM
Rwork0.215 ---
obs0.217 41665 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.95 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11857 0 0 0 11857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02212148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.94216435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28551480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68123.993596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.151152095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9061587
X-RAY DIFFRACTIONr_chiral_restr0.0860.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029338
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.25153
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.28167
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4551.57595
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.787211960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.90735125
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5874.54475
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
11C1508tight positional0.040.05
12B1508tight positional0.040.05
13D1508tight positional0.030.05
21C1316tight positional0.050.05
11C1503medium positional0.280.5
12B1503medium positional0.320.5
13D1503medium positional0.310.5
21C1292medium positional0.290.5
11C1508tight thermal0.050.5
12B1508tight thermal0.050.5
13D1508tight thermal0.050.5
21C1316tight thermal0.080.5
11C1503medium thermal0.362
12B1503medium thermal0.382
13D1503medium thermal0.382
21C1292medium thermal0.452
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 161 -
Rwork0.313 2982 -
obs--93.93 %

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