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- PDB-3ex4: human orotidyl-5'-monophosphate decarboxylase in complex with BMP -

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Basic information

Entry
Database: PDB / ID: 3ex4
Titlehuman orotidyl-5'-monophosphate decarboxylase in complex with BMP
ComponentsOrotidine-5'-phosphate decarboxylase
KeywordsLYASE / decarboxylase / tim barrel / unusual catalysis / Alternative splicing / Disease mutation / Glycosyltransferase / Multifunctional enzyme / 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 / 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsHeinrich, D. / 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
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: 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: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6402
Polymers28,3001
Non-polymers3401
Water6,215345
1
A: Orotidine-5'-phosphate decarboxylase
hetero molecules

A: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2804
Polymers56,5992
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3700 Å2
ΔGint-22.4 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.320, 116.900, 62.060
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-495-

HOH

21A-816-

HOH

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Components

#1: Protein Orotidine-5'-phosphate decarboxylase / OMPdecase


Mass: 28299.742 Da / Num. of mol.: 1 / Fragment: UNP residues 224-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→44.7 Å / Num. obs: 78072 / % possible obs: 98.9 % / Redundancy: 6.1 % / Rsym value: 0.075 / Net I/σ(I): 11.8
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 517 / Rsym value: 0.359 / % possible all: 47.1

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Processing

Software
NameVersionClassification
COMOphasing
REFMAC5.4.0077refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→38.66 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.984 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13507 3928 5.1 %RANDOM
Rwork0.11854 ---
obs0.11937 73733 98.49 %-
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: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.24→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 22 345 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222176
X-RAY DIFFRACTIONr_bond_other_d0.0020.021489
X-RAY DIFFRACTIONr_angle_refined_deg1.6072.0142974
X-RAY DIFFRACTIONr_angle_other_deg3.18433670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72323.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1111516
X-RAY DIFFRACTIONr_chiral_restr0.110.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022439
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02433
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_it1.4381.51346
X-RAY DIFFRACTIONr_mcbond_other0.7141.5554
X-RAY DIFFRACTIONr_mcangle_it2.18722182
X-RAY DIFFRACTIONr_scbond_it3.233830
X-RAY DIFFRACTIONr_scangle_it4.9394.5770
X-RAY DIFFRACTIONr_rigid_bond_restr1.52333665
X-RAY DIFFRACTIONr_sphericity_free7.2923345
X-RAY DIFFRACTIONr_sphericity_bonded3.01733607
LS refinement shellResolution: 1.24→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 245 -
Rwork0.246 4459 -
obs--81.58 %

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