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- PDB-8u0z: CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE... -

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Basic information

Entry
Database: PDB / ID: 8u0z
TitleCRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN OF Coffea arabica UMP SYNTHASE
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Coffea arabica / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
Function / homology
Function and homology information


orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / 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 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / 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 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
ANY 5'-MONOPHOSPHATE NUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesCoffea arabica (coffee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsHinojosa-Cruz, A. / Diaz-Vilchis, A. / Gonzalez-Segura, L.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN227920 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN211223 Mexico
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and functional properties of uridine 5'-monophosphate synthase from Coffea arabica.
Authors: Hinojosa-Cruz, A. / Diaz-Sanchez, A.G. / Diaz-Vilchis, A. / Gonzalez-Segura, L.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,80412
Polymers56,8982
Non-polymers90710
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-13 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.007, 95.699, 112.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uridine 5'-monophosphate synthase


Mass: 28448.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coffea arabica (coffee) / Gene: LOC113726974, LOC113732151 / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6P6VUE3, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase

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Non-polymers , 5 types, 615 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-N / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 214.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5 and 20% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.399→48.4 Å / Num. obs: 103974 / % possible obs: 97.3 % / Redundancy: 11.4 % / Biso Wilson estimate: 18.03 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.4
Reflection shellResolution: 1.399→1.47 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / Num. unique obs: 12799 / CC1/2: 0.89 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.399→47.849 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 5129 4.94 %
Rwork0.1581 --
obs0.1591 103831 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→47.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 58 606 4564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164186
X-RAY DIFFRACTIONf_angle_d1.4025676
X-RAY DIFFRACTIONf_dihedral_angle_d4.9312867
X-RAY DIFFRACTIONf_chiral_restr0.105631
X-RAY DIFFRACTIONf_plane_restr0.009737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.41490.30211320.28542318X-RAY DIFFRACTION70
1.4149-1.43160.29711510.25162701X-RAY DIFFRACTION80
1.4316-1.4490.2551580.22772866X-RAY DIFFRACTION87
1.449-1.46740.25991510.21843024X-RAY DIFFRACTION90
1.4674-1.48670.22651660.21183107X-RAY DIFFRACTION93
1.4867-1.5070.2521500.20373247X-RAY DIFFRACTION96
1.507-1.52860.22161450.19343313X-RAY DIFFRACTION98
1.5286-1.55140.20351600.18173360X-RAY DIFFRACTION100
1.5514-1.57560.22091620.1843370X-RAY DIFFRACTION100
1.5756-1.60150.19531940.18063315X-RAY DIFFRACTION100
1.6015-1.62910.21061910.17383334X-RAY DIFFRACTION100
1.6291-1.65870.21041740.173380X-RAY DIFFRACTION100
1.6587-1.69060.24371740.16973349X-RAY DIFFRACTION100
1.6906-1.72510.19831930.17323365X-RAY DIFFRACTION100
1.7251-1.76260.20381810.17373326X-RAY DIFFRACTION100
1.7626-1.80360.19441820.16883377X-RAY DIFFRACTION100
1.8036-1.84870.19791710.16973374X-RAY DIFFRACTION100
1.8487-1.89870.18451900.16553363X-RAY DIFFRACTION100
1.8987-1.95460.19851840.16023351X-RAY DIFFRACTION100
1.9546-2.01770.19221760.1553383X-RAY DIFFRACTION100
2.0177-2.08980.15541610.15293424X-RAY DIFFRACTION100
2.0898-2.17350.16451840.15773379X-RAY DIFFRACTION100
2.1735-2.27240.17861520.15393412X-RAY DIFFRACTION100
2.2724-2.39220.18421820.15913395X-RAY DIFFRACTION100
2.3922-2.54210.1581650.15723395X-RAY DIFFRACTION100
2.5421-2.73830.16351620.15683467X-RAY DIFFRACTION100
2.7383-3.01390.19351720.15783422X-RAY DIFFRACTION100
3.0139-3.44990.15551730.14643445X-RAY DIFFRACTION100
3.4499-4.3460.14692050.13093493X-RAY DIFFRACTION100
4.346-47.8490.17091880.15213647X-RAY DIFFRACTION100

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