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- PDB-3bgg: Crystal structure of Human Orotidine 5'-monophosphate Decarboxyla... -

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Basic information

Entry
Database: PDB / ID: 3bgg
TitleCrystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / UMP synthase / C-terminal Domain / Orotidine 5'-monophosphate Decarboxylase / human / BMP / 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 / 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLiu, Y. / Tang, H.L. / Wang, X.Y. / Kotra, L.P. / Pai, E.F.
CitationJournal: To be Published
Title: Crystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP
Authors: Liu, Y. / Tang, H.L. / Wang, X.Y. / Kotra, L.P. / Pai, E.F.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0922
Polymers31,7521
Non-polymers3401
Water2,378132
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1844
Polymers63,5032
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.596, 116.886, 61.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31751.604 Da / Num. of mol.: 1 / Fragment: Orotidine 5'-phosphate decarboxylase
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-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 / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
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: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 21306 / Num. obs: 20304 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.18 / Num. unique all: 818 / Rsym value: 0.5 / % possible all: 74.6

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Processing

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

2p1f


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.976 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.163 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21068 1048 5.1 %RANDOM
Rwork0.18126 ---
obs0.18274 19516 95.15 %-
all-21306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.081 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å20 Å2
2---2.37 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 22 132 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222087
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9892829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0962485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6531514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021549
X-RAY DIFFRACTIONr_nbd_refined0.2050.2992
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.217
X-RAY DIFFRACTIONr_mcbond_it1.0341.51361
X-RAY DIFFRACTIONr_mcangle_it1.45122106
X-RAY DIFFRACTIONr_scbond_it2.5873826
X-RAY DIFFRACTIONr_scangle_it4.144.5723
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 54 -
Rwork0.25 1039 -
obs-1093 68.44 %

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