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- PDB-7m0n: The crystal structure of wild type PA endonuclease (A/Vietnam/120... -

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Basic information

Entry
Database: PDB / ID: 7m0n
TitleThe crystal structure of wild type PA endonuclease (A/Vietnam/1203/2004) in complex with Raltegravir
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN/Inhibitor / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / VIRAL PROTEIN / VIRAL PROTEIN-Inhibitor complex
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / viral RNA genome replication / RNA binding / : / Chem-RLT / Protein PA-X
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Yun, M.K. / Dubois, R. / Rankovic, Z. / White, S.W.
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
History
DepositionMar 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein PA-X
B: Protein PA-X
C: Protein PA-X
D: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,11029
Polymers87,6644
Non-polymers3,44625
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-167 kcal/mol
Surface area34720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.702, 135.126, 126.751
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein PA-X


Mass: 21915.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/ruddy turnstone/New Jersey/Sg-00524/2008(H4N6))
Strain: A/ruddy turnstone/New Jersey/Sg-00524/2008(H4N6) / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: C6Y633

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Non-polymers , 5 types, 214 molecules

#2: Chemical
ChemComp-RLT / N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide / RALTEGRAVIR, MK0518


Mass: 444.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H21FN6O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiretroviral*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.5M ammonium sulfate, 2% PEG1500, 0.1 M Tris pH 8.0, and 1 mM MnCl2. then overnight crystals soak in 1.65 M ammonium sulfate, 2% PEG1500, 0.1 M Tris pH 8.0, 5 mM MnCl2, 10 mM MnCl2 and 20mM Raltegravir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97999 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97999 Å / Relative weight: 1
ReflectionResolution: 2.4→46.22 Å / Num. obs: 42607 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 53.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.037 / Rrim(I) all: 0.052 / Χ2: 0.93 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4317 / CC1/2: 0.771 / Rpim(I) all: 0.303 / Rrim(I) all: 0.718 / Χ2: 0.86 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E5F

4e5f


Resolution: 2.4→42.44 Å / SU ML: 0.3039 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8017
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: crazy
RfactorNum. reflection% reflection
Rfree0.2314 2099 4.94 %
Rwork0.1915 40425 -
obs0.1935 42524 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 206 189 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246293
X-RAY DIFFRACTIONf_angle_d0.52758487
X-RAY DIFFRACTIONf_chiral_restr0.0391883
X-RAY DIFFRACTIONf_plane_restr0.00381084
X-RAY DIFFRACTIONf_dihedral_angle_d18.62072390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.3191190.28662569X-RAY DIFFRACTION94.65
2.46-2.520.28081390.24222609X-RAY DIFFRACTION98.85
2.52-2.590.31330.23312681X-RAY DIFFRACTION99.08
2.59-2.660.2831400.23962667X-RAY DIFFRACTION99.5
2.66-2.750.36831370.26992678X-RAY DIFFRACTION99.82
2.75-2.850.3421260.2722705X-RAY DIFFRACTION99.93
2.85-2.960.29881390.24132679X-RAY DIFFRACTION99.96
2.96-3.090.30491410.23942710X-RAY DIFFRACTION99.89
3.09-3.260.28821480.25092681X-RAY DIFFRACTION100
3.26-3.460.29781390.2242704X-RAY DIFFRACTION99.96
3.46-3.730.24361300.18532745X-RAY DIFFRACTION99.97
3.73-4.10.21291390.15792707X-RAY DIFFRACTION100
4.1-4.70.18741360.14122733X-RAY DIFFRACTION99.93
4.7-5.910.1681620.16312740X-RAY DIFFRACTION99.97
5.91-42.440.18851710.17222817X-RAY DIFFRACTION98.84
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)
19.06418079317-1.365366214311.942782002276.361822948723.170435880636.04670319435-0.581298820898-0.1198017789580.774189784377-0.07772723206980.4340906629250.657385156332-0.772607136068-0.6283081485710.158835230890.7164934576240.2112011771920.08433186119330.4783415764470.2073616985760.638168569437-41.9454163468-3.4486617871724.8810451745
23.195933314590.3881186170882.626900463172.367109683270.8592254744854.15895526283-0.0434586846847-0.0515504104093-0.04257457164260.1541460661710.04022612762010.3071573408910.455170672606-0.06822388359870.01326277312450.5911841765420.02109952927760.1314203730880.4332930715890.2182361915180.489257272209-47.7147218058-19.568782152217.1423790598
38.063476371310.7964489509211.16046569956.60722107085-0.9576941904218.685000611120.0594984371422-0.7378773943240.20482852670.225527497948-0.2965818407920.3689573009710.5700040882-1.034740708570.1854455988670.9637665161160.01074411714630.07815017149530.6163230742040.1656663704460.46268014096-48.0136632618-27.226337151427.9167367963
44.112570425953.052220771952.467308354936.408876166253.65204194864.199706400990.0805219059914-0.114947995178-0.5271455892510.3982626109140.259870731788-0.5451321309610.3490847395010.23780356273-0.318073339020.6334070318010.1823153848360.08084753808540.496909261480.2125879174680.446181838439-33.0504580107-22.536363858425.2500613345
54.33773996823-0.396077589497-0.7099645741142.956642487392.065627243633.4798903139-0.083512798964-0.282275640645-0.3115443857150.7249386916840.2229646862190.718085356145-0.158245360888-1.17046529239-0.1281408588581.129611200140.04951638596430.1685051207621.018570483910.1720700228320.552386255093-42.9360342966-14.325375240136.9664782691
69.16189871363-1.22910834807-3.682694217547.70696701920.6163822759059.060498692980.1146169041090.4266995227771.10183310489-0.3636921025940.571761631291-0.404405412607-1.228596462580.0881601178093-0.7284439111090.620779137308-0.142330236502-0.07883048245050.365216463170.1002519924350.659185233881-53.625388067-4.66050006517-9.02431213064
79.77493948967-5.6154271092-0.03894821734713.420640742810.2435158831852.259577609260.06315618185510.7355621256250.607215759286-0.262309430147-0.142360028919-0.17571833753-0.199748104111-0.2701266856770.1389094961680.574464239122-0.184009847383-0.1084050721250.5374157309740.1195710760090.640597656132-55.055617808-11.277181931-11.1180732536
84.865255739331.05870261986-3.896112106034.74679692381-1.292492318336.03232492678-0.02153049047320.321600331279-0.267855847452-0.33652963608-0.009678740326580.1269974158350.19909435468-0.1360556857450.06769988041480.412918360151-0.154493236233-0.07552275976060.38779395996-0.07184888244980.492456072284-45.3948922042-22.6843188454-19.0739911121
98.39498500652.8940566427-4.142343685157.62653259616-2.8314276452.33221950729-0.6768287079830.7149105435790.202000393973-0.6350746510150.1703053117630.4884459227020.992954621735-1.492204446340.5295203733080.688664707221-0.24639638272-0.01408690576720.707973591782-0.06306576117051.03215395564-61.5830977092-28.0383749268-16.9999216936
106.574770342450.352518997566-0.5264830643255.64609930502-3.35918658432.155645490850.32715099967-0.0091644308294-0.467143259292-0.358086804415-0.0236918479072-0.14556666445-0.236049982560.525209808324-0.23610329390.474564909998-0.219658976954-0.005023106355050.443040751161-0.03424311497740.799211264053-53.1087680922-28.9747816901-15.496516566
112.28942892002-2.82463845837-2.013841090945.144641886452.114032695793.96676086954-0.217513478136-0.143511011921-0.2820719576890.4551541855690.02856013348230.4104391091740.343388150663-0.1866637296910.2101786537570.426689495294-0.1592915825690.008474000380770.4548347431540.1373520097880.670449444051-55.3208113793-23.3187549368-1.63977709118
124.75328705081-3.41197050344-3.007795572378.818140170930.4213693469462.35255910158-0.0283189777331.2011606063-0.49324438217-0.6196719039-0.2084703329162.03090940360.373579988659-2.218407297940.1864917003310.589194644271-0.160768841387-0.2134598276191.003960648220.05650081892171.09828533182-69.5150101869-15.0649146439-9.15796721222
133.724868634121.84574920598-2.123838160315.809263040112.637455348733.916762100550.0770820340883-0.8915823968070.427932300080.4578321803620.568110383059-0.490235289946-1.002530528040.634815424859-0.7022294300590.6861003252370.131286486287-0.1040201560640.644776165746-0.1716564239750.617472433267-5.7347344124-3.8641940560310.7661794073
144.266644038641.08618344097-2.020799849141.624906135950.04195852367913.88109720628-0.157899840003-0.27502083724-0.520456490140.3427742460880.133638442813-0.07909038316750.05442704201130.01643757956590.03326744938220.4580798489710.207874456209-0.04879309916380.4291960096610.02884355943290.520451367062-14.3223579395-19.59499187417.7118349066
152.925227251591.57468369027-0.6628124382265.08983893709-1.619954577343.00556874006-0.286608789773-0.125098013125-0.5310408020930.2202778676310.129810066943-0.2741485029340.273957186710.2148504616450.1349574099870.4900868672070.195923183558-0.01272421753990.496361820456-0.09608848245210.59408259935-5.23692099272-24.75516822829.12264126338
165.56683140354-0.5254418159161.443049475596.76167758822-2.046209881625.781883486550.113522763272-1.0500842253-0.3390393766760.8972336087230.230492086283-0.5617039090750.1169951645673.16520335061-0.3017346718310.544684212310.109439743566-0.1278849880361.13158946829-0.07848703409940.9558145389258.4517270072-15.07877381412.7519582471
174.12213088205-0.5220075480182.519951752757.11123306959-4.627948050218.96028891115-0.372662359380.5165328563130.397386391001-0.2871187733120.208384837457-0.359648335208-0.4011115108860.6279028965280.1716265981870.548886323243-0.1139011366170.08088138434890.428864507212-0.1235730348810.440840778542-20.475955879-8.64570446457-23.4608355927
186.027532430930.387194718684.291094153073.92629195441.254075662165.671525678710.177392609285-0.0319891328159-0.148978006982-0.1589920979340.0192149546899-0.3179184278160.410185730650.223351981126-0.1845841715370.5596240756810.04912669092870.02958858263630.392671045318-0.1806405818520.49533195341-11.0607710254-22.5782874342-13.9055677162
195.949822176822.633927383230.250511986247.29394407685-0.9175877911615.794507963710.1250838616760.235364702794-0.5058163528250.177558659618-0.125494070405-1.127075162020.7088663549020.8208534039-0.05817896377880.7461043003710.0214260394475-0.02905454363810.664473924335-0.3082297339440.641381650437-13.435200672-28.9657582235-25.8935496201
204.90680826222-1.331900618361.932023334556.70320867406-4.007935035464.052928593150.05970753582180.436520543692-0.393265428752-0.469252066080.217975161875-0.2490375398720.633722411774-0.210950532067-0.2848652101740.561698030184-0.11039370391-0.008192262510750.415129168082-0.1818881143450.431240112896-28.3530596698-23.9121959345-23.8858562276
216.99468733144-0.328397543716-1.414432483554.54745195745-2.299440276751.501215438510.05909160754541.89032994678-0.869508370832-0.9976221149190.223038379232-0.3980061304840.5708155410721.79817730989-0.1916084479950.98737882012-0.02694967511740.1152890313911.36024240631-0.186455150120.609547628236-19.1213979236-16.0797088237-33.4769542229
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )AA1 - 311 - 31
22chain 'A' and (resid 32 through 126 )AA32 - 12632 - 107
33chain 'A' and (resid 127 through 149 )AA127 - 149108 - 130
44chain 'A' and (resid 150 through 185 )AA150 - 185131 - 166
55chain 'A' and (resid 186 through 203 )AA - B186 - 301167
66chain 'B' and (resid 1 through 23 )BC1 - 231 - 23
77chain 'B' and (resid 24 through 50A)BC24 - 5024 - 51
88chain 'B' and (resid 50B through 126 )BC50 - 12652 - 107
99chain 'B' and (resid 127 through 138 )BC127 - 138108 - 119
1010chain 'B' and (resid 139 through 149 )BC139 - 149120 - 130
1111chain 'B' and (resid 150 through 185 )BC150 - 185131 - 166
1212chain 'B' and (resid 186 through 202 )BC186 - 202167 - 183
1313chain 'C' and (resid 1 through 31 )CG1 - 311 - 31
1414chain 'C' and (resid 32 through 126 )CG32 - 12632 - 107
1515chain 'C' and (resid 127 through 185 )CG127 - 185108 - 166
1616chain 'C' and (resid 186 through 205 )CG186 - 205167 - 186
1717chain 'D' and (resid 1 through 50A)DI1 - 501 - 51
1818chain 'D' and (resid 50B through 126 )DI50 - 12652 - 107
1919chain 'D' and (resid 127 through 149 )DI127 - 149108 - 130
2020chain 'D' and (resid 150 through 185 )DI150 - 185131 - 166
2121chain 'D' and (resid 186 through 202 )DI - M186 - 304167

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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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