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- PDB-3mi2: Crystal structure of human orotidine-5'-monophosphate decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 3mi2
TitleCrystal structure of human orotidine-5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / UMP synthase / Orotidine 5'-monophosphate Decarboxylase / pyrazofurin monophosphate
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / 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 / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / 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
Chem-PFU / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLiu, Y. / To, T. / Kotra, L.P. / Pai, E.F.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase.
Authors: Meza-Avina, M.E. / Wei, L. / Liu, Y. / Poduch, E. / Bello, A.M. / Mishra, R.K. / Pai, E.F. / Kotra, L.P.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 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
B: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6874
Polymers61,0082
Non-polymers6782
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-26 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.485, 62.109, 70.499
Angle α, β, γ (deg.)90.00, 111.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase / Orotate phosphoribosyltransferase / OPRTase / Orotidine 5'-phosphate decarboxylase / OMPdecase


Mass: 30504.162 Da / Num. of mol.: 2
Fragment: Orotidine 5'-monophosphate Decarboxylase Domain (UNP residues 223-480)
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-PFU / (1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol / Pyrazofurin Monophosphate


Mass: 339.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2010
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: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.2→65.62 Å / Num. obs: 147972 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 2.56 / Num. unique all: 8204 / Rsym value: 0.288 / % possible all: 46.9

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Processing

Software
NameVersionClassification
MxDCdata collection
MOLREPphasing
REFMAC5.5.0109refinement
Coot0.6.2-pre-1model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1F

2p1f


Resolution: 1.2→65.62 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.72 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19247 7408 5 %RANDOM
Rwork0.17051 ---
obs0.1716 140506 84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.33 Å2
2---0.46 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.2→65.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 44 692 4674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224475
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9926102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06123.989183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57215826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5611531
X-RAY DIFFRACTIONr_chiral_restr0.1130.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213409
X-RAY DIFFRACTIONr_mcbond_it0.7171.52806
X-RAY DIFFRACTIONr_mcangle_it1.31124548
X-RAY DIFFRACTIONr_scbond_it2.21331669
X-RAY DIFFRACTIONr_scangle_it3.6194.51554
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 312 -
Rwork0.271 5482 -
obs-5794 44.88 %

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