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- PDB-2jgy: The crystal structure of human orotidine-5'-decarboxylase domain ... -

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Basic information

Entry
Database: PDB / ID: 2jgy
TitleThe crystal structure of human orotidine-5'-decarboxylase domain of human uridine monophosphate synthetase (UMPS)
ComponentsUMP SYNTHASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / ALTERNATIVE SPLICING / LYASE / POLYMORPHISM / DECARBOXYLASE / DISEASE MUTATION / TIM BARREL DIMER / OROTIDINE-5'-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
Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Ericsson, U.B. / Flodin, S. ...Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Orotidine-5'-Decarboxylase Domain of Human Uridine Monophosphate Synthetase (Umps)
Authors: Moche, M. / Flodin, S. / Nyman, T. / Stenmark, P. / Nordlund, P.
History
DepositionFeb 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UMP SYNTHASE
B: UMP SYNTHASE


Theoretical massNumber of molelcules
Total (without water)61,2622
Polymers61,2622
Non-polymers00
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.830, 77.830, 152.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UMP SYNTHASE / OROTATE PHOSPHORIBOSYLTRANSFERASE / OPRTASE / OROTIDINE 5'-PHOSPHATE DECARBOXYLASE / OMPDECASE


Mass: 30631.232 Da / Num. of mol.: 2
Fragment: OROTIDINE-5'-DECARBOXYLASE DOMAIN OF UMPS, RESIDUES 224-479
Source method: isolated from a genetically manipulated source
Details: THE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO THE N-TERMINAL LINKER BETWEEN THE START OF THE DECARBOXYLASE DOMAIN (GLU224) AND THE HEXAHISTIDINE TAIL
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO ...THE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO THE N-TERMINAL LINKER BETWEEN THE START OF THE DECARBOXYLASE DOMAIN (GLU224) AND THE N-TERMINAL HEXAHISTIDINE TAIL

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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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0408
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2006 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
RadiationMonochromator: BENT SILICON CRYSTAL, HORIZONTALLY FOCUSING. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 58331 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.24 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DQW

1dqw


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.482 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT, HOWEVER, NCS HAS NOT BEEN USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2662 5.1 %RANDOM
Rwork0.158 ---
obs0.16 49980 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.26 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 0 671 4471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223979
X-RAY DIFFRACTIONr_bond_other_d0.0010.022736
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9795382
X-RAY DIFFRACTIONr_angle_other_deg0.89236696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71523.333156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15315735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9751529
X-RAY DIFFRACTIONr_chiral_restr0.0750.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_nbd_refined0.2060.2835
X-RAY DIFFRACTIONr_nbd_other0.1950.22988
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21963
X-RAY DIFFRACTIONr_nbtor_other0.0830.22035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5123295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65934057
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63241643
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.73451325
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.201 207
Rwork0.165 3641

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