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- PDB-3bk0: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 3bk0
TitleCrystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with 5-CN-UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / UMP Synthase / C-terminal Domain / Orotidine 5'-monophosphate Decarboxylase / Human / 5-CN-UMP / Disease mutation / Glycosyltransferase / Multifunctional enzyme / 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 / 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
5-CYANO-URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Tang, H.L. / Avina, M.E.M. / Kotra, L.P. / Pai, E.F.
CitationJournal: To be Published
Title: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with 5-CN-UMP
Authors: Liu, Y. / Tang, H.L. / Avina, M.E.M. / Kotra, L.P. / Pai, E.F.
History
DepositionDec 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_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_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

Downloads & links

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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)62,0198
Polymers60,9442
Non-polymers1,0756
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.552, 61.554, 70.989
Angle α, β, γ (deg.)90.00, 111.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30472.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CNU / 5-CYANO-URIDINE-5'-MONOPHOSPHATE / 5-cyano-UMP / 5-cyanouridine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 349.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N3O9P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
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: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 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: 1.6→50 Å / Num. all: 58529 / Num. obs: 58523 / % possible obs: 78.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 1.95 / Num. unique all: 1607 / Rsym value: 0.323 / % possible all: 21.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Coot0.1-3-pre-1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1F

2p1f


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.785 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21562 2938 5 %RANDOM
Rwork0.17919 ---
obs0.18102 55585 78.25 %-
all-58529 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å21.85 Å2
2---1.27 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 68 256 4258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224325
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9925880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32823.873173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7915780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7491530
X-RAY DIFFRACTIONr_chiral_restr0.10.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023236
X-RAY DIFFRACTIONr_nbd_refined0.2110.22191
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2325
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.218
X-RAY DIFFRACTIONr_mcbond_it0.9691.52810
X-RAY DIFFRACTIONr_mcangle_it1.48624385
X-RAY DIFFRACTIONr_scbond_it2.47531701
X-RAY DIFFRACTIONr_scangle_it3.9514.51495
LS refinement shellResolution: 1.6→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 49 -
Rwork0.275 969 -
obs-1018 18.57 %

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