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- PDB-3g3d: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 3g3d
TitleCrystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-azido-UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / UMP synthase / c-terminal Domain / Orotidine 5'-monophosphate Decarboxylase / human / 5-fluoro-6-azido-UMP / Decarboxylase / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Phosphoprotein / 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 / cytoplasm / cytosol
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: 1.7 Å
AuthorsLiu, Y. / Tang, H.L. / Bello, A. / Poduch, E. / Kotra, L. / Pai, E.
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: Non-polymer description / 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
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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1658
Polymers68,1082
Non-polymers1,0576
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-44 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.682, 61.850, 70.320
Angle α, β, γ (deg.)90.00, 112.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34054.156 Da / Num. of mol.: 2
Fragment: UNP residues 190-480, 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.: 2 / Source method: obtained synthetically / Formula: C9H12FN2O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2007 / Details: Monochromator Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 61223 / Num. obs: 58024 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.765 / Num. unique all: 1859 / Rsym value: 0.493 / % possible all: 61.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.4.0066refinement
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: 1.7→28.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.729 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20978 2927 5 %RANDOM
Rwork0.17544 ---
obs0.17724 54927 94.78 %-
all-58131 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.924 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å23 Å2
2---1.43 Å20 Å2
3---2.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 67 331 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224405
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9945992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44123.859184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4615786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0741533
X-RAY DIFFRACTIONr_chiral_restr0.1080.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213333
X-RAY DIFFRACTIONr_mcbond_it0.7441.52754
X-RAY DIFFRACTIONr_mcangle_it1.3624446
X-RAY DIFFRACTIONr_scbond_it2.32531651
X-RAY DIFFRACTIONr_scangle_it3.7694.51546
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 159 -
Rwork0.301 2753 -
obs--64.55 %

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