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- PDB-2vr2: Human Dihydropyrimidinase -

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Basic information

Entry
Database: PDB / ID: 2vr2
TitleHuman Dihydropyrimidinase
ComponentsDIHYDROPYRIMIDINASE
KeywordsHYDROLASE / HYDANTOINASE / METAL-BINDING / DISEASE MUTATION / DIHYDROPYRIMIDINE AMIDOHYDROLASE / DIHYDROPYRIMIDINASE / NUCLEOTIDE METABOLISM / DHP / DPYS / DHPASE / ZN-BINDING
Function / homology
Function and homology information


thymine binding / pyrimidine nucleoside catabolic process / pyrimidine nucleobase catabolic process / uracil binding / dihydropyrimidinase / thymine catabolic process / dihydropyrimidinase activity / uracil catabolic process / beta-alanine metabolic process / Pyrimidine catabolism ...thymine binding / pyrimidine nucleoside catabolic process / pyrimidine nucleobase catabolic process / uracil binding / dihydropyrimidinase / thymine catabolic process / dihydropyrimidinase activity / uracil catabolic process / beta-alanine metabolic process / Pyrimidine catabolism / amino acid binding / phosphoprotein binding / protein-containing complex / extracellular exosome / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWelin, M. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Welin, M. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Dihydropyrimidinase
Authors: Welin, M. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Welin, M. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Nordlund, P.
History
DepositionMar 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 6, 2015Group: Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
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_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_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: DIHYDROPYRIMIDINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4334
Polymers59,2661
Non-polymers1663
Water181
1
A: DIHYDROPYRIMIDINASE
hetero molecules

A: DIHYDROPYRIMIDINASE
hetero molecules

A: DIHYDROPYRIMIDINASE
hetero molecules

A: DIHYDROPYRIMIDINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,73116
Polymers237,0664
Non-polymers66512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area15460 Å2
ΔGint-70.2 kcal/mol
Surface area73770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.650, 89.650, 219.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DIHYDROPYRIMIDINASE / / DHPASE / DHP / DIHYDROPYRIMIDINE AMIDOHYDROLASE / HYDANTOINASE


Mass: 59266.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q14117, dihydropyrimidinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS CO-CRYSTALLIZED IN THE PRESENCE OF CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN ...THE PROTEIN WAS CO-CRYSTALLIZED IN THE PRESENCE OF CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN THE CRYSTAL IS AAPSRLLIRG GRVVNDDFSE VADVLVEDGV VRALGHDLLP PGGAPAGLRV LDAAGKLVLP GGIDTHTHMQ FPFMGSRSID DFHQGTKAAL SGGTTMIIDF AIPQKGGSLI EAFETWRSWA DPKVCCDYSL HVAVTWWSDQ VKEEMKILVQ DKGVNSFKMF MAYKDLYMVT DLELYEAFSR CKEIGAIAQV HAENGDLIAE GAKKMLALGI TGPEGHELCR PEAVEAEATL RAITIASAVN CPLYIVHVMS KSAAKVIADA RRDGKVVYGE PIAASLGTDG THYWNKEWHH AAHHVMGPPL RPDPSTPDFL MNLLANDDLT TTGTDNCTFN TCQKALGKDD FTKIPNGVNG VEDRMSVIWE KGVHSGKMDE NRFVAVTSTN AAKIFNLYPR KGRIAVGSDA DIVIWDPKGT RTISAKTHHQ AVNFNIFEGM VCHGVPLVTI SRGKVVYEAG VFSVTAGDGK FIPRKPFAEY IYKRIKQRDR TCTPTPVERA PYKGEVATL

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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: 2.33 Å3/Da / Density % sol: 47.35 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2007 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 13425 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 17.23 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.63
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 17.94 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 6.01 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FTW

2ftw


Resolution: 2.8→19.95 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 34.948 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 38-48 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 682 5.1 %RANDOM
Rwork0.2 ---
obs0.203 12742 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å22.23 Å20 Å2
2--4.45 Å20 Å2
3----6.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 3 1 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9451.9445120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9115476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05423.62163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4115630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9951524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.170.21714
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22556
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1521.52418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.27323821
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.32131522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5414.51299
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
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 43
Rwork0.313 881
Refinement TLS params.Method: refined / Origin x: 33.2677 Å / Origin y: -15.0606 Å / Origin z: -20.2493 Å
111213212223313233
T-0.1482 Å20.0035 Å20.0234 Å2-0.0047 Å2-0.147 Å2---0.0836 Å2
L1.3546 °20.0399 °2-0.1525 °2-1.2594 °2-0.0466 °2--1.8809 °2
S-0.0534 Å °0.1909 Å °-0.1937 Å °-0.266 Å °-0.1482 Å °0.2629 Å °0.3662 Å °-0.2504 Å °0.2015 Å °

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