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- PDB-2p1f: Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate ... -

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Basic information

Entry
Database: PDB / ID: 2p1f
TitleHuman UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase)
ComponentsUridine 5'-monophosphate synthase
KeywordsHYDROLASE / UMP synthase / C-terminal Domain / Orotidine 5'-Monophosphate Decarboxylase / human
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / '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 / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / 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
Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLiu, Y. / Tang, H.L. / Pai, E.F.
CitationJournal: TO BE PUBLISHED
Title: Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase)
Authors: Liu, Y. / Tang, H.L. / Pai, E.F.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2557
Polymers31,7681
Non-polymers4876
Water5,350297
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,51014
Polymers63,5352
Non-polymers97512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6280 Å2
ΔGint-88 kcal/mol
Surface area19400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.314, 116.875, 61.946
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-2029-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: X, -Y, -Z.

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Components

#1: Protein Uridine 5'-monophosphate synthase


Mass: 31767.600 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2.28M 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: 1.76→65.09 Å / Num. all: 28427 / Num. obs: 26969 / % possible obs: 99.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.49 / Num. unique all: 1392 / Rsym value: 0.459 / % possible all: 100

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Processing

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

2eaw


Resolution: 1.76→65.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.752 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17067 1435 5.1 %RANDOM
Rwork0.13949 ---
obs0.14113 26969 99.64 %-
all-28427 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.76→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 30 297 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222290
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9853113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12423.91897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6981518
X-RAY DIFFRACTIONr_chiral_restr0.1040.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021747
X-RAY DIFFRACTIONr_nbd_refined0.230.21207
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.228
X-RAY DIFFRACTIONr_mcbond_it0.9671.51484
X-RAY DIFFRACTIONr_mcangle_it1.45422332
X-RAY DIFFRACTIONr_scbond_it2.6593893
X-RAY DIFFRACTIONr_scangle_it4.3294.5781
LS refinement shellResolution: 1.76→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 99 -
Rwork0.163 1905 -
obs-2004 96.3 %

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