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

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Basic information

Entry
Database: PDB / ID: 6tai
TitleCrystal structure of Escherichia coli Orotate Phosphoribosyltransferase with an empty active site at 1.55 Angstrom resolution
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate phosphoribosyltransferase (OPRT)
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 / cytoplasm / cytosol
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
ACETATE ION / Orotate phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 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 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 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.page_first / _citation.page_last / _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)47,3414
Polymers47,1902
Non-polymers1512
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-16 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.464, 131.752, 39.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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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(DE3) (bacteria)
References: UniProt: P0A7E3, orotate phosphoribosyltransferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.03 % / Description: Cubic, bipyramidal, and rhombohedral plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% (w/v) PEG 6000, 0.2 M MgCl2, 0.1 M sodium acetate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.03076 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 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: 1.03076 Å / Relative weight: 1
ReflectionResolution: 1.55→65.569 Å / Num. obs: 57472 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Net I/σ(I): 20.8
Reflection shellResolution: 1.551→1.556 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 510 / CC1/2: 0.68 / Rpim(I) all: 0.407 / Rrim(I) all: 0.997 / % possible all: 89.5

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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 1ORO

1oro


Resolution: 1.551→65.48 Å / SU ML: 0.1935 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5704
RfactorNum. reflection% reflection
Rfree0.2036 2807 4.89 %
Rwork0.1768 --
obs0.1781 57394 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 1.551→65.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 10 195 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043290
X-RAY DIFFRACTIONf_angle_d0.68884443
X-RAY DIFFRACTIONf_chiral_restr0.0442501
X-RAY DIFFRACTIONf_plane_restr0.0041580
X-RAY DIFFRACTIONf_dihedral_angle_d22.84181207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.34970.312547X-RAY DIFFRACTION91.58
1.58-1.610.28371260.26272662X-RAY DIFFRACTION98.13
1.61-1.640.2731460.24462649X-RAY DIFFRACTION97.49
1.64-1.670.25531160.23592700X-RAY DIFFRACTION98.6
1.67-1.710.2461460.23342713X-RAY DIFFRACTION99.44
1.71-1.750.28791170.2272669X-RAY DIFFRACTION98.48
1.75-1.790.24771490.22512738X-RAY DIFFRACTION99.14
1.79-1.840.2721500.21552666X-RAY DIFFRACTION99.22
1.84-1.890.23191560.20682718X-RAY DIFFRACTION98.86
1.89-1.950.22931290.20052716X-RAY DIFFRACTION100
1.95-2.020.25471350.19252737X-RAY DIFFRACTION99.17
2.02-2.10.22191640.18982706X-RAY DIFFRACTION99.38
2.1-2.20.21661440.18952759X-RAY DIFFRACTION99.55
2.2-2.320.19011370.17172736X-RAY DIFFRACTION99.83
2.32-2.460.21311600.17722747X-RAY DIFFRACTION99.66
2.46-2.650.21731470.1832761X-RAY DIFFRACTION99.52
2.65-2.920.22191520.18082760X-RAY DIFFRACTION99.79
2.92-3.340.19841470.17042797X-RAY DIFFRACTION99.63
3.34-4.210.16051320.14942849X-RAY DIFFRACTION99.57
4.21-65.480.18011570.15812957X-RAY DIFFRACTION98.89
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)
10.8237118622830.379185829596-0.3454209301140.497750852466-0.3559566566410.30732892711-0.1430195886140.116777524763-0.132369901424-0.04464211741190.120868390925-0.3420127778520.02825693251180.3587236085650.007320498099070.222724277142-0.0566772680886-4.35397161299E-50.2558488695180.02499646045680.27995993545110.876374257314.5393669857-21.6884442405
21.24495161934-0.224439531557-0.3826240714410.427417033094-0.5606856629620.546360511392-0.09258432495480.02954367647440.03749848853770.06737964938830.00150152467829-0.0614905464393-0.0502488431113-0.0012652396343-1.9697257199E-50.216794393862-0.0206939051579-0.04365255558980.22030235822-0.02176547327290.272499008185-0.36094197633120.5045743113-14.8525701024
30.2142165923570.04817066570890.08790892320040.01402822163420.01674326831560.00905893262669-0.06129839528020.00885982983990.07147271936750.00205143020282-0.0261153878301-0.0358737823615-0.236698013094-0.0162720781347-0.0002117030174040.229460377732-0.0184692883828-0.02556103481370.210177819158-0.02183710007450.211739847439-6.0991665500520.2566682369-10.8541721046
40.984447219081-0.431436515206-0.3213585580390.628396088571-0.09365459498720.2322264764520.142387705530.1521681407080.3682588855940.07007473862470.0589524323936-0.0502735039560.00614463798646-0.2340674156254.55108653966E-50.2865691324880.0344030327354-0.01898536628720.2656619840450.02136745565880.355803359671-9.1286078906130.2446270092-19.2324153987
50.2056540357020.13120537245-0.2134697341910.09578994948230.1341977528010.931937642643-0.1621350022250.02111841477910.22350208636-0.20356604316-0.1563178806550.190483701948-0.6039002537230.148313081498-0.07110011494220.413141771767-0.0333771286792-0.1065311662860.2110765331240.07084888450240.410884702867.3791090934229.8763983015-26.5188589823
60.4076826721360.3449719118590.4013549934080.2991579508620.1511051791450.387161033992-0.0944044599065-0.08703606919390.0158439766118-0.142350627622-0.156586374554-0.5951592187610.01439107152630.327466812149-0.001982274811410.247325801124-0.0203682516540.056348432560.3485405360550.127855811640.37346922721320.700162467117.520701372-24.1263722546
70.617503412280.375449521194-0.2089560230190.552187255825-0.09631143848680.2696379858910.00745780977802-0.2484799222910.05509353599770.1406669477510.08752155851470.333035900885-0.132251587784-0.05500331684270.0001714610762810.246247716087-0.0125109579862-0.01428774181990.224883785497-0.008956067967110.22159036183-30.32236089817.8655344907-2.32077813677
80.704895251304-0.212752281177-0.8352599349730.09794477213140.2500438091070.4759177087770.0250729734402-0.05206261764210.2005694144440.04031990162990.0663330919482-0.0574432547797-0.09463036111640.09932884105690.0001607989353570.257834969618-0.021410280566-0.004568537954810.232441107522-0.01554960345520.191395872349-19.522628395715.5843467863-5.15735927135
91.064915112810.497801661983-0.5816579744560.9264635130660.4175352437661.30565742174-0.08008237932420.150881510695-0.150444427338-0.0950640554450.01845259792330.0230706410197-0.0039707846476-0.02095607795253.32884478743E-50.200504759572-0.00912979782133-0.004759102925370.218191513701-0.01466726254160.189114813297-13.84068196728.56258312328-16.6713598833
100.581505492567-0.308009272136-0.02646551100210.3174442240660.0499110737860.0859747896648-0.152609295655-0.554512984117-0.3623770873160.0375364976150.3316799187340.3793976849690.198344587479-0.4622347270110.006368777048040.3015285425860.02946851307620.009501113659290.3214010532730.02499956864190.172667386898-22.55409268846.30639941289-26.0845482397
110.266446795035-0.0760124399663-0.08958381242620.580452521236-0.260759549978-0.0523626978567-0.154083057510.0230040282327-0.166728894053-0.1465656818850.08321682641930.162686593776-0.0950966568539-0.02393564966799.23738825475E-60.222937536508-0.02563210052940.001707058109580.242987912328-0.04640789442490.238497629037-30.20953392175.05712450702-14.4610687407
120.539154404964-0.339634781539-0.05802169735940.361925782622-0.245651223660.492518747796-0.0110508435787-0.359589137436-0.2455393381280.3083600291260.02907481938240.4553380186620.10935826789-0.2932438206610.05561668794070.29771023878-0.001156993452890.08327251144510.339689332494-0.02898337354310.247563828103-38.7040414313.94383503942.46115259221
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 72 )
3X-RAY DIFFRACTION3chain 'AAA' and (resid 73 through 88 )
4X-RAY DIFFRACTION4chain 'AAA' and (resid 89 through 152 )
5X-RAY DIFFRACTION5chain 'AAA' and (resid 153 through 183 )
6X-RAY DIFFRACTION6chain 'AAA' and (resid 184 through 213 )
7X-RAY DIFFRACTION7chain 'BBB' and (resid 1 through 32 )
8X-RAY DIFFRACTION8chain 'BBB' and (resid 33 through 60 )
9X-RAY DIFFRACTION9chain 'BBB' and (resid 61 through 132 )
10X-RAY DIFFRACTION10chain 'BBB' and (resid 133 through 142 )
11X-RAY DIFFRACTION11chain 'BBB' and (resid 143 through 183 )
12X-RAY DIFFRACTION12chain 'BBB' and (resid 184 through 213 )

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