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- PDB-3g3m: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 3g3m
TitleCrystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Human / Orotidine 5'-monophosphate Decarboxylase / c-terminal Domain / 5-fluoro-6-iodo-UMP / Alternative splicing / Decarboxylase / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Phosphoprotein / Polymorphism / Pyrimidine biosynthesis / Transferase
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-FLUORO-URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLiu, Y. / Tang, H.L. / Bello, A.M. / Poduch, E. / Kotra, L.P. / Pai, E.F.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents.
Authors: Bello, A.M. / Konforte, D. / Poduch, E. / Furlonger, C. / Wei, L. / Liu, Y. / Lewis, M. / Pai, E.F. / Paige, C.J. / Kotra, L.P.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8302
Polymers30,4881
Non-polymers3421
Water4,900272
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6614
Polymers60,9762
Non-polymers6842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5140 Å2
ΔGint-32 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 116.558, 62.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase


Mass: 30488.162 Da / Num. of mol.: 1
Fragment: UNP residues 223-480, Orotidine 5'-phosphate decarboxylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: gi|13960142, OK/SW-cl.21, UMPS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-5FU / 5-FLUORO-URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 342.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / pH: 8.4
Details: Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2007
Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 50630 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.213 / % possible all: 60.7

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Processing

Software
NameVersionClassification
MxDCdata collection
MOLREPphasing
REFMAC5.2.0019refinement
Coot0.1.3-pre-1model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1F

2p1f


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.869 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 2643 5.1 %RANDOM
Rwork0.15891 ---
obs0.16007 49620 93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.312 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 22 272 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4231.9873176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87924.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44415432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4281515
X-RAY DIFFRACTIONr_chiral_restr0.1650.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211787
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21672
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1911.51463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87222380
X-RAY DIFFRACTIONr_scbond_it3.1963862
X-RAY DIFFRACTIONr_scangle_it4.8234.5796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 122 -
Rwork0.284 2281 -
obs--58.57 %

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