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- PDB-3l0n: Human orotidyl-5'-monophosphate decarboxylase in complex with 6-m... -

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Basic information

Entry
Database: PDB / ID: 3l0n
TitleHuman orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Decarboxylase / Multifunctional enzyme / Pyrimidine biosynthesis
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
6-sulfanyluridine-5'-phosphate / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHeinrich, D. / Wittmann, J. / Diederichsen, U. / Rudolph, M.
CitationJournal: Chemistry / Year: 2009
Title: Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Authors: Heinrich, D. / Diederichsen, U. / Rudolph, M.G.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 26, 2010ID: 3EX5
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)57,3124
Polymers56,5992
Non-polymers7122
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-22 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.644, 62.165, 69.935
Angle α, β, γ (deg.)90.00, 113.99, 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: 28299.742 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 224-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-S5P / 6-sulfanyluridine-5'-phosphate / 6-mercaptouridine-5'-monophosphate


Mass: 356.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACCORDING TO AUTHORS, THE LIGAND S5P HAS DISTORTED GEOMETRY UPON BINDING TO THE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 1.8M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.762
11L, -K, H20.238
ReflectionResolution: 1.74→34.65 Å / Num. obs: 53875 / % possible obs: 97.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 26.463 Å2 / Rsym value: 0.078 / Net I/σ(I): 12.6
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2192 / Rsym value: 0.575 / % possible all: 80

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Processing

SoftwareName: REFMAC / Version: 5.6.0041 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→34.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.147 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20737 2714 5 %RANDOM
Rwork0.18047 ---
obs0.18182 51149 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.011 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20 Å214.96 Å2
2---14.23 Å20 Å2
3---19.57 Å2
Refinement stepCycle: LAST / Resolution: 1.74→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 44 262 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224060
X-RAY DIFFRACTIONr_bond_other_d0.0010.022770
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9915493
X-RAY DIFFRACTIONr_angle_other_deg0.98536782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62123.964169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1115732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2451528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0260.222555
X-RAY DIFFRACTIONr_mcbond_other0.0210.242955
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 153 -
Rwork0.385 2559 -
obs--65.91 %

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