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- PDB-6tak: Crystal structure of Escherichia coli Orotate Phosphoribosyltrans... -

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Basic information

Entry
Database: PDB / ID: 6tak
TitleCrystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid and Sulfate at 1.25 Angstrom resolution
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate phosphoribosyltransferase (OPRT) / Orotic acid / Sulfate
Function / homology
Function and homology information


pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
OROTIC ACID / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNavas-Yuste, S. / Lopez-Estepa, M. / Gomez, S. / Fernandez, F.J. / Vega, M.C.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2015-66206-C2-2-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-1018-102242-B-I00 Spain
Spanish National Research Council2016E064 Spain
CitationJournal: Acs Catalysis / Year: 2020
Title: Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X-ray Crystallography and Computational Simulations
Authors: Roca, M. / Navas-Yuste, S. / Zinovjev, K. / Lopez-Estepa, M. / Gomez, S. / Fernandez, F.J. / Vega, M.C. / Tunon, I.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Orotate phosphoribosyltransferase
BBB: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,91919
Polymers47,1902
Non-polymers1,72917
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-154 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.658, 69.469, 104.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Orotate phosphoribosyltransferase / / OPRTase


Mass: 23594.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pyrE, b3642, JW3617 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0A7E3, orotate phosphoribosyltransferase
#2: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.44 % / Description: Cubic, bipyramidal, and rhombohedral plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 2.1 M (NH4)2SO4, 0.2 M NaCl, 0.3 M sodium citrate (pH 4.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2019 / Details: Kirkpatrick-Baez (KB) focusing mirrors
RadiationMonochromator: Channel-cut Si(111), cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.25→47.72 Å / Num. obs: 452457 / % possible obs: 95.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Net I/σ(I): 13.2
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.386 / Num. unique obs: 12799 / CC1/2: 0.292 / Rpim(I) all: 1.001 / Rrim(I) all: 1.722 / % possible all: 68.8

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSMar 15, 2019 BUILT=20190315data reduction
Aimless0.7.4data scaling
PHASER2.8.2 (svn 8393)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wwPDB 6TAI

6tai


Resolution: 1.25→47.72 Å / SU ML: 0.2551 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.2545
RfactorNum. reflection% reflection
Rfree0.2059 1982 1.96 %
Rwork0.1811 --
obs0.1816 101164 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.23 Å2
Refinement stepCycle: LAST / Resolution: 1.25→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 103 375 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01183550
X-RAY DIFFRACTIONf_angle_d1.21324813
X-RAY DIFFRACTIONf_chiral_restr0.0818529
X-RAY DIFFRACTIONf_plane_restr0.008618
X-RAY DIFFRACTIONf_dihedral_angle_d15.88711339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.5036910.46214568X-RAY DIFFRACTION60.44
1.28-1.310.591860.53464155X-RAY DIFFRACTION55.31
1.31-1.350.46341430.4177151X-RAY DIFFRACTION94.81
1.35-1.40.39881490.38397471X-RAY DIFFRACTION98.94
1.4-1.450.29631510.30547567X-RAY DIFFRACTION99.6
1.45-1.50.29161490.24237504X-RAY DIFFRACTION99.62
1.5-1.570.27531510.22377557X-RAY DIFFRACTION99.45
1.57-1.660.2391520.20237605X-RAY DIFFRACTION99.92
1.66-1.760.22341510.16957563X-RAY DIFFRACTION99.87
1.76-1.890.21041520.17567597X-RAY DIFFRACTION99.61
1.89-2.090.21971460.18147358X-RAY DIFFRACTION96.06
2.09-2.390.21031480.1587438X-RAY DIFFRACTION97
2.39-3.010.17161540.15477731X-RAY DIFFRACTION99.58
3.01-47.720.15261590.14967917X-RAY DIFFRACTION98.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05069470278-0.779942305585-0.2625638628631.74410586755-0.3369833133671.23578484555-0.0208647867836-0.450199384316-0.1743650602850.3738538073570.03479295219960.02225155020950.125965869248-0.195573748361-0.03398352485520.289113534833-0.0473205411712-0.01914312350950.2767359463640.0447933960770.07728968631598.051822085875.601878537336.6765979497
21.04004598474-0.2037175087560.5593169272480.7637461193770.3404558418951.605717711430.0185517509607-0.0801376669944-0.0351593226242-0.0272746862831-0.0444639333697-0.00359401639847-0.0738217567708-0.02791452218830.01335727069390.177947114098-0.00430840850507-0.003512332499190.1248724110910.01587432251130.03102364808357.288678833786.3346425697519.5434534665
35.959820935841.32721548076-2.010388346653.0836223202-1.307994280414.10231674537-0.3104339671520.373961607159-0.795106380556-0.4414757122540.1544911377160.3089456771810.658347359179-0.04666441831460.2370662460510.3786255438480.0362636304101-0.04456599389640.224580237643-0.08332253097340.2312917561827.2460364651-7.915715358359.82948571191
41.19401571745-0.898137261622-1.275617332561.89075206769-0.6476537101039.136347246470.0414743975171-0.0244416137698-0.3080752347730.391519385817-0.1864165856130.0497953232193-0.04544075717030.09160342653180.0007466133032710.250743463985-0.0150089795246-0.004386023060090.18131708405-0.005488868889940.14241147709713.8452021298-1.5645641944821.682682305
52.75838621949-0.958665999083-1.972098967891.99987873640.929193946291.4464852146-0.167548023854-0.280832445254-0.589775330120.205475503246-0.5008522463660.06491874376170.9348282107340.8495907667080.2802988178420.4608600770390.00383192214444-0.0275161977610.3779026620660.05123944093350.20862446435915.6709995031-10.152310947216.1796948731
60.8467582537430.5056153163710.483085938790.3282934774460.4874499100872.347536725910.00671409284991-0.0376280677426-0.2368333172550.1080512106510.0639658106529-0.1591483020610.2969225272770.687478304817-0.05355601647920.2933380597760.0663390807455-0.0163400434970.2831550979120.01153650141580.09428987645120.6749808697-2.0268527683527.5075633788
70.7573276368420.1383516057990.02081061518981.49573009193-0.5192994451132.08546226574-0.0785299037784-0.4487712714530.01107891518170.6256253865640.2309818852190.0407262551437-0.166892452741-0.1476486658190.04549253795650.4231885476850.0607031413851-0.01784418825370.3367935653940.00804162832030.087880927261614.55223384117.076177206944.5698078449
82.968413883740.7580127201010.3652934440631.86513056328-0.05362844373752.470898703330.01003459428150.248801642371-0.175039522388-0.1735186426770.0447913467342-0.0149424138866-0.00336113812974-0.0220975676489-0.054551594410.2311837025710.0274496420587-0.02690487060890.157590106190.01257540454960.0539786668547-7.624679576414.44890195987-4.26043943016
91.55075850390.01019540340710.3380598024470.4365774651160.05521562241863.030928288320.01990776879670.0173105595897-0.00425587858829-0.03121578271080.01757212329180.0194974233568-0.0763449639080.000469725356292-0.02683580994960.1799811620220.00896354527615-0.0158784879780.09764381379640.01518279594950.0529808000322-5.889455758377.74086694096.15165916474
101.24690628142-0.0906571787761-0.103502699662.35760408945-0.07334531503062.234996129480.00862486994432-0.177200859985-0.1574291451580.0492110359775-0.0137777693715-0.04208801266990.0935806072717-0.157624734868-0.03030526221580.1976356337920.0032633284982-0.00542467775310.1638854424740.01593731751860.0660159351641-8.67140223640.46774428004219.5056682365
114.835280724080.196197804052-1.434276513564.41998888345-2.572047670581.858623129290.02332277272950.464735179827-0.174503014163-0.7222395539650.1240111916260.2310940903920.0195747668718-0.193929618624-0.08851950619760.3458328245990.00860523774654-0.04326822004920.2181027116360.03883900115240.159420307418-15.7439129301-9.6577526761616.9743457809
120.9179174129940.0667695916564-0.7949407562190.0622413446516-0.3215220963614.03532286927-0.0871485849170.0660787543009-0.184429765689-0.1311859169660.04292629821440.08218928520030.337614909961-0.3547717898030.05859626425310.265350526254-0.0338994494824-0.01453475332750.1803686195670.01978789066410.114500505818-19.1397379391-3.162263776695.50354448556
133.426243948441.9333254164-2.348014715832.17582364143-2.317958906533.55367632422-0.05562149654750.00200790932451-0.0139457949743-0.1156236656470.04570535968990.1523131769380.0870083995505-0.3362838896130.004105585731190.2480753215140.0215329292971-0.03055144843410.2604417688340.01726799234830.0689422542787-21.7370058386-1.362051639267.3254659227
142.932437931620.3560810382520.7656349129095.308778422610.8134512671383.537105312910.09561362151090.3648562198420.151001340479-0.1389657725590.00501531182954-0.197954452946-0.073035776756-0.123544535141-0.066592201740.2569813138620.0386820282205-0.02580374591370.1872101581440.03126843354660.0489291272802-14.61225418396.03271461777-11.7477100513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'AAA' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'AAA' and (resid 33 through 98 )
3X-RAY DIFFRACTION3chain 'AAA' and (resid 99 through 118 )
4X-RAY DIFFRACTION4chain 'AAA' and (resid 119 through 130 )
5X-RAY DIFFRACTION5chain 'AAA' and (resid 131 through 143 )
6X-RAY DIFFRACTION6chain 'AAA' and (resid 144 through 183 )
7X-RAY DIFFRACTION7chain 'AAA' and (resid 184 through 213 )
8X-RAY DIFFRACTION8chain 'BBB' and (resid 1 through 32 )
9X-RAY DIFFRACTION9chain 'BBB' and (resid 33 through 60 )
10X-RAY DIFFRACTION10chain 'BBB' and (resid 61 through 130 )
11X-RAY DIFFRACTION11chain 'BBB' and (resid 131 through 142 )
12X-RAY DIFFRACTION12chain 'BBB' and (resid 143 through 165 )
13X-RAY DIFFRACTION13chain 'BBB' and (resid 166 through 183 )
14X-RAY DIFFRACTION14chain 'BBB' and (resid 184 through 213 )

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