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

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Basic information

Entry
Database: PDB / ID: 6taj
TitleCrystal structure of Escherichia coli Orotate Phosphoribosyltransferase in complex with Orotic acid 1.60 Angstrom resolution
ComponentsOrotate phosphoribosyltransferase
KeywordsTRANSFERASE / Orotate phosphoribosyltransferase (OPRT) / Orotic acid
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: 1.6 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 2.0May 26, 2021Group: Atomic model / Category: atom_site / Item: _atom_site.label_alt_id
Revision 2.1Jun 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 2.2Jan 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)47,6866
Polymers47,1902
Non-polymers4964
Water3,459192
1
AAA: Orotate phosphoribosyltransferase
hetero molecules

AAA: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6866
Polymers47,1902
Non-polymers4964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3920 Å2
ΔGint-11 kcal/mol
Surface area17590 Å2
MethodPISA
2
BBB: Orotate phosphoribosyltransferase
hetero molecules

BBB: Orotate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6866
Polymers47,1902
Non-polymers4964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3580 Å2
ΔGint-16 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.118, 83.118, 122.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Components on special symmetry positions
IDModelComponents
11AAA-408-

HOH

21AAA-509-

HOH

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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-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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.21 Å3/Da / Density % sol: 44.44 % / Description: Cubic, bipyramidal, and rhombohedral plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: 1.6→49.38 Å / Num. obs: 57672 / % possible obs: 99.5 % / Redundancy: 12.5 % / Biso Wilson estimate: 29.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Net I/σ(I): 15.1 / Num. measured all: 720144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6411.22.2644423339470.4420.6952.3720.893.6
7.14-49.3810.60.03682337780.9990.0110.03845.699.8

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3206refinement
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: 1.6→49.38 Å / SU ML: 0.2407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.374
RfactorNum. reflection% reflection
Rfree0.2234 2000 3.49 %
Rwork0.1949 --
obs0.1959 57358 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.88 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 34 192 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093365
X-RAY DIFFRACTIONf_angle_d0.85264555
X-RAY DIFFRACTIONf_chiral_restr0.0561507
X-RAY DIFFRACTIONf_plane_restr0.006596
X-RAY DIFFRACTIONf_dihedral_angle_d17.08132032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.35411280.36013540X-RAY DIFFRACTION90.39
1.64-1.680.37351410.31583905X-RAY DIFFRACTION100
1.68-1.730.30141420.30363933X-RAY DIFFRACTION99.95
1.73-1.790.30931410.27173908X-RAY DIFFRACTION99.98
1.79-1.850.24851430.2453930X-RAY DIFFRACTION100
1.85-1.920.26841420.24283935X-RAY DIFFRACTION100
1.92-2.010.26821410.22883935X-RAY DIFFRACTION100
2.01-2.120.27971440.22423973X-RAY DIFFRACTION100
2.12-2.250.24381430.21193959X-RAY DIFFRACTION100
2.25-2.420.22161430.20713961X-RAY DIFFRACTION100
2.42-2.670.25391450.20764001X-RAY DIFFRACTION100
2.67-3.050.20441460.19934031X-RAY DIFFRACTION100
3.05-3.850.21191470.17664061X-RAY DIFFRACTION99.98
3.85-49.380.19021540.15964286X-RAY DIFFRACTION99.95
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)
10.00565836006769-0.00203128890603-0.004850496813210.001800690163170.002931483696240.008776828348450.0220822570487-0.105847304384-0.0527402486282-0.0361562344569-0.118428153306-0.005246750704920.09056441570460.1090168741232.46657685497E-50.365123127455-0.02364156436380.02222426940290.3615771014680.09476679248540.28933230213130.496219326142.226368845247.906992305
20.139796415323-0.0274536978592-0.01921087864460.00613204873193-0.004170607236620.01284922264540.0893017592028-0.1007482855040.1502574975380.255000838845-0.1028089051840.2953826183340.000620112255281-0.0758056937238-0.0143122832390.42515944443-0.1514472485870.1768410697220.395747039501-0.08745583903950.37414210016120.355056200755.003157304855.9149534424
30.04464220690470.009366763232770.04297930372430.03229529233260.005527160578240.04201439166120.0963718080835-0.201219334807-0.08405985819320.199725366877-0.179342137667-0.03746141816640.120005721220.0869166174252-7.58585399768E-50.253589185959-0.03872824859410.03086514970610.2559757017930.02492716279160.2392399388528.039265895348.537426670641.5198418481
40.01424614334640.008354828723140.007605098505420.0059344129553-0.003121155050360.0145378563991-0.0807758435465-0.0482626398787-0.0644087041171-0.03132613452150.004780734394530.002068801540560.0638462028636-0.0564758383227-4.98848227966E-50.269354556795-0.01044815448120.01166205881090.233286571406-0.01558353126060.29298563850417.796094706146.972045871929.4797925635
50.01495736363860.016803559328-0.001537484111090.0316507481903-0.02608963728690.01881630259930.00236468101443-0.09361695258290.01981277056590.121968935716-0.158866395210.03642426277630.08459065197120.009230059826053.08272449761E-50.2428034153650.006369808186450.04420559020330.1979103828210.0312393802340.2317159148228.016663392347.941198053631.4168980875
60.008187796682440.00136963689665-0.009379065246720.00808599900367-0.02331414472460.0563913534968-0.204751407290.0814400337560.1323862640560.01654487090580.0780439273442-0.01775032495920.0836056929889-0.1330537212454.16130123255E-50.2924546102720.0208577748456-0.02472440441940.2389717991870.0004045555901860.30624750270318.650286613452.025291723824.1320701349
70.007702728393020.003790076369050.001294455152210.00849932375208-0.00688892523020.00608760277306-0.111303707368-0.2303631251780.155121955401-0.02211614040080.0774134338250.002653555783290.0108806047553-0.122913333659-0.0001752066305150.264583503989-0.00586155261970.005338240062970.311452349542-0.03635536128980.36651846890514.720593710148.743362712437.188828658
80.001753864555980.001049869462620.002194496213950.0005068447221420.0002880803037010.0005061174463350.0191393747475-0.01763204225810.113589636196-0.042528365376-0.03501858595690.02948351381690.00403256165602-0.08607126420731.23902011057E-50.2749245582860.0029368924562-0.001377406606410.356513672716-0.03702356090070.3891001051926.7130223652.708832624730.4294606822
90.150136482135-0.1708506923460.06967166964390.302808983826-0.1114668993570.03715930006840.150072194534-0.2066379964920.0921409507760.0875485374326-0.1576944946460.470515888776-0.0188951637755-0.2181363211940.05065028732590.284537491402-0.08199684526940.08139143189330.387620053793-0.04474544929020.37635554565611.00499774444.688651534943.1521692792
100.00803816894586-0.0143318865757-0.005356539531480.02719903672220.01085988323410.00440143755534-0.02291843044220.0114661521308-0.0002104762778170.101986953258-0.0845597605079-0.05850741699160.0642632168775-0.028820621827-0.06814613718920.652844890557-0.200662424680.01432945386530.5171042361050.09727133107230.24170538777525.635991452439.921201856956.3419005758
110.0322603401518-0.00325088314296-0.00878481990098-0.00670167004136-0.008414844715270.00906466511204-0.00302181471724-0.040872148245-0.06068278852050.203240306969-0.02916805802260.03972880109720.0891265930942-0.007911568545360.02075427617970.653775114868-0.6544218115920.4979290026660.7978662265580.0460763416673-0.10660302936319.850082789144.469582082462.0958375945
120.127177973420.05250311705790.08794566767730.02981601005910.03191337473040.257964956571-0.1090416471350.100514770065-0.00979269608849-0.300779240221-0.02550898553580.00820205704846-0.2296712944480.183309506862-0.08291788277710.440425769612-0.0518783248238-0.1302067525020.2256761485040.0008773869289780.37871442552534.751071555319.325235327122.1908517032
130.155394905928-0.001638394326780.1537952497450.008812117833350.006384841462690.129986569943-0.0894732995014-0.1003979059530.0241896060771-0.3632621371240.08595611747070.168938573341-0.16563842158-0.04529110508570.01704296809980.393882088292-0.0736719863545-0.06608009061660.2382774932290.0007358539196360.29254049882639.700436250627.309111882327.7449704888
140.7137307402830.7648505448530.570425625350.7834970753220.5990587010170.4733252301110.121762211638-0.4885385220010.1347152116680.108184417034-0.617509732019-0.050839325860.2365955783110.113395743635-0.2663689554920.2963220365320.004674650789420.04716624331380.3667457171620.05462704045210.28893523614446.270916317329.292280195637.2265066249
150.3481893217810.3094994976020.3770480312910.272167982390.3343468150780.4045665447490.03099591373-0.3394468708390.04694522420760.147042962801-0.487719370098-0.1150387731890.000623627461002-0.023428861067-0.2495776482590.341695335623-0.183920824972-0.0645592824280.6760519175760.2395868077880.42953306872353.485843611529.329264368741.9215774312
160.02693408111380.00910140379257-0.02617575907470.0798129730999-0.09066559491130.123678728520.0912034582227-0.113019825604-0.27146240961-0.151294669138-0.390035053718-0.1481947115540.1388298088680.268212538694-0.005012336998990.45438770106-0.101170156555-0.09578347276720.5864840396920.1041428583080.41776000304344.681838645819.234026635537.28300221
170.0497987401559-0.00884940969072-0.07484678564510.01252978980860.0282480608640.137521916658-0.1052092244760.0524568223248-0.1055533274010.0201966100426-0.1293110477240.01206022568620.08244479937320.0355117701121-0.01616695187530.573540708412-0.0421110082754-0.29892567860.5661884077020.3089286312741.1513733781952.317583997413.632957844441.4976621256
180.0171102521937-0.0158697098135-0.05205696195130.1077561487220.01498289932450.1643656790670.02608834939040.0354449049698-0.0435198809607-0.00599321237016-0.179507314395-0.132184350401-0.0295989513915-0.0405587729992-0.1058096945420.513489045606-0.138655426913-0.2420900519740.4742442126980.1651083522480.38936603313246.427149447720.483673532844.2748417908
190.190667133275-0.0188955687528-0.05510299942720.01987221400710.03149053688010.04454703256040.08341758098650.00318719559005-0.1263221113470.10756955921-0.264237344892-0.189594621467-0.07745711202820.137765735273-0.02284390739970.467081334126-0.0733758561499-0.1555896481980.2257594728040.05665195368510.34747320890337.862413098810.9492833936.637538601
200.00264830490230.00335524293057-0.004544397046280.00258429432048-0.004771391200650.004235881626720.01300346602440.06526542063750.01701416028490.101733339364-0.0737402993358-0.0434990949973-0.0136121810932-0.100996715111-4.21831720528E-50.401205063320.0590365956181-0.1188561550860.302725731683-0.07181302674720.3520530805324.538441075418.559247205624.6193136719
210.01611521542610.01874150492260.01953328418770.02423846221340.02878344067830.0242356377873-0.03267601665210.0825907074045-0.175312490437-0.0304716413067-0.103591913322-0.0224061565426-0.145701715435-0.0796596541309-6.08334513517E-50.356348487172-0.0190849033301-0.07745147266880.2689060842760.005728482367040.3344527564326.866161689410.741283259520.7050313918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'AAA' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'AAA' and (resid 15 through 32 )
3X-RAY DIFFRACTION3chain 'AAA' and (resid 33 through 60 )
4X-RAY DIFFRACTION4chain 'AAA' and (resid 61 through 72 )
5X-RAY DIFFRACTION5chain 'AAA' and (resid 73 through 89 )
6X-RAY DIFFRACTION6chain 'AAA' and (resid 90 through 118 )
7X-RAY DIFFRACTION7chain 'AAA' and (resid 119 through 130 )
8X-RAY DIFFRACTION8chain 'AAA' and (resid 131 through 143 )
9X-RAY DIFFRACTION9chain 'AAA' and (resid 144 through 183 )
10X-RAY DIFFRACTION10chain 'AAA' and (resid 184 through 194 )
11X-RAY DIFFRACTION11chain 'AAA' and (resid 195 through 213 )
12X-RAY DIFFRACTION12chain 'BBB' and (resid 1 through 32 )
13X-RAY DIFFRACTION13chain 'BBB' and (resid 33 through 60 )
14X-RAY DIFFRACTION14chain 'BBB' and (resid 61 through 89 )
15X-RAY DIFFRACTION15chain 'BBB' and (resid 90 through 118 )
16X-RAY DIFFRACTION16chain 'BBB' and (resid 119 through 129 )
17X-RAY DIFFRACTION17chain 'BBB' and (resid 130 through 142 )
18X-RAY DIFFRACTION18chain 'BBB' and (resid 143 through 152 )
19X-RAY DIFFRACTION19chain 'BBB' and (resid 153 through 183 )
20X-RAY DIFFRACTION20chain 'BBB' and (resid 184 through 194 )
21X-RAY DIFFRACTION21chain 'BBB' and (resid 195 through 213 )

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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