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

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Basic information

Entry
Database: PDB / ID: 3bvj
TitleCrystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with XMP
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Human / UMP Synthase / Orotidine 5'-monophosphate Decarboxylase / XMP / 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
XANTHOSINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y. / Tang, H.L. / Pai, E.F.
CitationJournal: To be Published
Title: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with XMP
Authors: Liu, Y. / Tang, H.L. / Pai, E.F.
History
DepositionJan 7, 2008Deposition 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)69,1237
Polymers68,1082
Non-polymers1,0155
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.857, 61.976, 70.514
Angle α, β, γ (deg.)90.00, 112.96, 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: 34054.156 Da / Num. of mol.: 2 / Fragment: OMPdecase, residues 190-480
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-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
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: 1.8→50 Å / Num. all: 50616 / Num. obs: 49502 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 6.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.64 / Num. unique all: 4656 / Rsym value: 0.456 / % possible all: 90.9

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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: 1.8→24.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.071 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22844 2579 5.1 %RANDOM
Rwork0.18505 ---
obs0.18723 48026 97.31 %-
all-49353 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å21.77 Å2
2---1.04 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 64 311 4309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224255
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9925773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24623.779172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45415769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0981530
X-RAY DIFFRACTIONr_chiral_restr0.1040.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023166
X-RAY DIFFRACTIONr_nbd_refined0.2020.22197
X-RAY DIFFRACTIONr_nbtor_refined0.30.22962
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.214
X-RAY DIFFRACTIONr_mcbond_it1.0011.52766
X-RAY DIFFRACTIONr_mcangle_it1.37724283
X-RAY DIFFRACTIONr_scbond_it2.35431704
X-RAY DIFFRACTIONr_scangle_it3.7164.51490
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 170 -
Rwork0.345 3022 -
obs-3192 83.41 %

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