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- PDB-7zgw: Serratia NucC apo form -

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Basic information

Entry
Database: PDB / ID: 7zgw
TitleSerratia NucC apo form
ComponentsSerratia NucC
KeywordsRNA BINDING PROTEIN / Nuclease
Function / homologyDomain of unknown function DUF6602 / Domain of unknown function (DUF6602) / DUF6602 domain-containing protein
Function and homology information
Biological speciesSerratia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGarcia-Doval, C. / Mayo-Munoz, D. / Smith, L.M. / Fineran, P.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden FundMFP-UOO2011 New Zealand
CitationJournal: Mol.Cell / Year: 2022
Title: Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection.
Authors: Mayo-Munoz, D. / Smith, L.M. / Garcia-Doval, C. / Malone, L.M. / Harding, K.R. / Jackson, S.A. / Hampton, H.G. / Fagerlund, R.D. / Gumy, L.F. / Fineran, P.C.
History
DepositionApr 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Feb 7, 2024Group: 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: Serratia NucC
B: Serratia NucC
D: Serratia NucC
C: Serratia NucC
E: Serratia NucC
F: Serratia NucC


Theoretical massNumber of molelcules
Total (without water)173,3806
Polymers173,3806
Non-polymers00
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, NucC forms an hexamer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24300 Å2
ΔGint-124 kcal/mol
Surface area48420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.468, 95.492, 94.536
Angle α, β, γ (deg.)90.000, 92.052, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Serratia NucC


Mass: 28896.703 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: CWC46_19930, Ser39006_019925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TBB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 5.5 10% PEG 8000 10% PEG 1000 0.8 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.83→42.61 Å / Num. obs: 124878 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Net I/σ(I): 23.7
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6266 / CC1/2: 0.832 / Rpim(I) all: 0.304

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSBUILT 20190806data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q1H
Resolution: 1.83→42.61 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 6326 5.07 %
Rwork0.1671 118541 -
obs0.1692 124867 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.27 Å2
Refinement stepCycle: LAST / Resolution: 1.83→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11029 0 0 797 11826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010111230
X-RAY DIFFRACTIONf_angle_d1.0115218
X-RAY DIFFRACTIONf_chiral_restr0.05791727
X-RAY DIFFRACTIONf_plane_restr0.01031973
X-RAY DIFFRACTIONf_dihedral_angle_d13.94584114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.26031840.22854000X-RAY DIFFRACTION99.9
1.85-1.870.31042310.23423880X-RAY DIFFRACTION99.88
1.87-1.890.28482070.23313973X-RAY DIFFRACTION99.95
1.89-1.920.28092110.23623897X-RAY DIFFRACTION100
1.92-1.940.27862170.22753927X-RAY DIFFRACTION99.95
1.94-1.970.28722120.22123950X-RAY DIFFRACTION100
1.97-20.27872040.21853933X-RAY DIFFRACTION99.95
2-2.030.25671990.18493955X-RAY DIFFRACTION100
2.03-2.060.20661960.16953939X-RAY DIFFRACTION99.98
2.06-2.090.21712080.16933953X-RAY DIFFRACTION99.98
2.09-2.130.22812000.1693930X-RAY DIFFRACTION100
2.13-2.170.20712350.16393953X-RAY DIFFRACTION99.98
2.17-2.210.22771970.16753949X-RAY DIFFRACTION99.98
2.21-2.250.23172150.1693908X-RAY DIFFRACTION100
2.25-2.30.2152310.16683927X-RAY DIFFRACTION99.98
2.3-2.360.20992200.17243942X-RAY DIFFRACTION99.95
2.36-2.410.22542050.16973934X-RAY DIFFRACTION100
2.41-2.480.2492040.18463972X-RAY DIFFRACTION100
2.48-2.550.23062420.1783900X-RAY DIFFRACTION99.98
2.55-2.630.25482030.17613991X-RAY DIFFRACTION100
2.63-2.730.20122350.16833915X-RAY DIFFRACTION99.98
2.73-2.840.20061970.16613944X-RAY DIFFRACTION99.98
2.84-2.970.21642270.17983960X-RAY DIFFRACTION99.98
2.97-3.120.22681860.1763946X-RAY DIFFRACTION99.98
3.12-3.320.21382210.17493960X-RAY DIFFRACTION99.93
3.32-3.580.18442180.15583973X-RAY DIFFRACTION99.9
3.58-3.930.17762300.15443956X-RAY DIFFRACTION99.88
3.93-4.50.16282170.13183972X-RAY DIFFRACTION99.9
4.5-5.670.17611590.1384037X-RAY DIFFRACTION99.79
5.67-42.610.18982150.16724065X-RAY DIFFRACTION99.84
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.617306781210.25584279431-0.2523698378991.11929621813-0.2449432322931.006393512730.05031920040890.0809934695764-0.105661061953-0.0398121040896-0.0486912962363-0.06636452691580.07065315452620.0202926571167-0.0006454922964770.17587114344-0.00119896888452-0.02416137193580.200774783313-0.007462752884810.202399082406-13.6521729768-20.4797900612-51.7844402692
22.836902140493.63061073182-0.4526695441835.50683540703-0.1601192536520.967076194395-0.00642774648714-0.0574925986580.0675323710163-0.0319619702731-0.0623174713261-0.147099577936-0.04386104437230.1457866493020.07401440282950.143525189676-0.0040048333749-0.03398340703360.2053905171380.0002248925468350.209370009161-0.801506408954-11.7614311994-43.5810263787
31.579021120331.2055044983-0.7019500769291.86585009391-0.7154780604541.294582773180.0754411153189-0.1392651229780.01930869566680.169038517766-0.0935881952488-0.06659859242490.04458760405350.00802452075640.03533113995790.163691501858-0.0349057587375-0.03069277275590.176994855077-0.01955255743960.200675163943-12.1696150513-17.5304884812-39.0607401719
43.722198798383.44194486250.4430063851356.1796615778-0.6809108267782.56067721751-0.00162683361390.08905899752610.323891756153-0.255783815570.001520416962520.4856622875310.123539929605-0.295898739201-0.007161971747690.2748767368860.1246357955410.0110125667370.235646642698-0.02067959193020.242567741022-35.98735584690.130635861552-76.6208625716
51.04428031712-0.436797289380.6180005876211.00553635939-0.4879389820591.598240555310.03790985668350.01962021422610.114229390287-0.0995157355934-0.08086709003860.0042541646681-0.14941521427-0.1020591801720.03715702953870.16727582970.0471303555178-0.0007600189130760.152934661647-0.02998619005910.214975161633-34.72043484473.99145228252-57.6022441986
66.36188073177-1.27302593833.963698924795.95910365744-2.190934045518.719009572560.09696593189850.452087373137-0.0890564312296-0.423814756789-0.163764536709-0.1865753594370.2565418804950.4093037557250.06382224591590.196648241703-0.002441991291150.09284594097190.251660694411-0.01185131767960.3300258459775.85338540103-15.8337640865-73.6515354213
73.09636437916-0.63845553337-0.1587416464671.524599172630.1464192350481.69625052910.06103313377830.2790414881580.161189764463-0.282313742335-0.0732022503532-0.0777312984777-0.1981051784340.0310480702237-0.0359570343760.270884869761-0.006950641524680.05012535771160.2174839892960.05592986617710.23228687051-7.284023379783.52477592257-76.0363671742
81.278004595971.149413152370.3830285160251.3149686719-0.4746949674883.04593233440.06945983234230.6536061602060.640804986301-0.444842098780.0322991979697-0.821297536247-0.2142239587190.727528515210.002576623426820.418956148616-0.04854788678720.231914202370.5430799691490.1115576290850.67695133839913.53831151842.79178107915-80.5171777123
92.82569389889-0.9399150065930.1909765242882.29968036962-0.00087226673120.929684695358-0.03107004424950.005577464484130.364627789089-0.08651859793470.0580514801194-0.414957736369-0.1566096826280.1588165487390.02215241174970.269280788234-0.02574302168540.08886146008260.2023348191650.04272285112860.2763117518660.6029206705664.66912502886-70.1034021852
107.30035203011-5.4036230916-1.075752947326.287918026920.9596726293373.52995360193-0.0631871625958-0.167078388916-0.13945589304-0.09622265802840.0241599398350.372926337068-0.0981292857122-0.1322719303060.0526294799390.156769620573-0.0568559975938-0.04935271726540.268847279582-0.004986050633050.239621874888-36.6389328005-27.4209670262-54.2010310694
112.27169820071-1.50346368996-0.9391004122634.665968580530.6968137676723.807151130260.0600982535362-0.02970509697060.291277221590.122482248676-0.114284302557-0.0492409189797-0.526562633837-0.1066240088580.09524335420330.286805585573-0.00846823231073-0.0725633224030.263355748156-0.04674636107910.305673242561-37.7457448027-19.84956914-63.8749510901
120.9130411047470.397646772-0.09463764077771.43214931195-0.8295247067812.932831723950.1334227667320.166636657110.0693445197168-0.171221851414-0.1705071836530.184670576334-0.204656169361-0.2761037956220.03545582677760.2414063376020.0726778814329-0.09454123380250.290879039631-0.0738116210320.253288824389-42.3622172837-20.0033214701-76.2680497248
132.283705693470.846054514856-0.824135464820.931651667608-2.067468620755.33558396095-0.006113767295130.276642536102-0.132354528889-0.505488632386-0.07900482992590.239498232510.205636400079-0.4422153189340.02596106086360.4382402676920.088923690859-0.2085097820760.419495077291-0.1314449101630.321607578877-45.2578097132-26.9678472098-88.5949918089
144.555060047412.020207349190.1705362501355.19863618467-1.491927081130.613174793910.124585117173-0.3793793888320.1119462820310.389517895157-0.1267694497661.026929734070.0688483063128-0.966132000312-0.04706929655730.256523949559-0.0137573870990.03932648948020.589286032266-0.107132460260.492559031658-56.2882189907-29.1816117268-62.7068468192
151.366731344130.1760547689220.04053726832192.32562754727-1.541482697343.374588456240.1955136346990.107090975468-0.160734993464-0.259856683746-0.1808579242530.4848909136610.0316841868569-0.401477936232-0.1229353744750.2180871939080.0206254377873-0.1019753418190.364347853992-0.09701103661410.408631831968-50.6108090039-29.799852613-68.1905557198
162.172150453020.501065804591-0.08020431605091.98221778783-1.009237641643.937076622370.1071302572910.150404015841-0.45575069636-0.0454598811966-0.1699872757170.3305855954540.516010241943-0.207967527790.04915414440350.232486579837-0.0351670591629-0.06181424520450.262032026338-0.07473124867630.329341183452-43.3892008023-36.8163240161-66.6351911921
171.060877719310.292913812541-0.2391535819662.87147294622-1.575886684363.0294123376-0.1079165720850.516725986766-0.0100650423807-0.61218776620.0704436740577-0.1961529556030.159948331039-0.1329132065480.08016351338580.5133883213060.122323043638-0.1352496329190.480158163395-0.05528565247860.324026498149-37.9203735628-19.8116016501-93.7673160266
181.975731136380.403584835399-0.1671471030981.169864691210.1295553602631.083826481960.1130920933120.0371460674092-0.0427870317925-0.118841539833-0.080809570587-0.1320165705360.04924804912620.178111648181-0.02527296609460.2323898236490.06611029333110.001684022380470.217143334854-0.01447611225220.293274210207-3.31708574933-29.2699514127-68.4024279955
195.05669005458-0.3100148976070.2022839891490.5833046829120.4050525277071.308391728620.117203582856-0.116515865257-0.1185985455850.036484448495-0.0713762594372-0.03016787979180.065431659798-0.0483910534741-0.04171651821320.198532873180.0111975357324-0.06264770717190.127190424318-0.01772424506840.23910381146-15.4653726657-39.4777008304-63.7417332482
207.28138173924-0.6248297944187.253158455020.241023137515-0.8243192097887.82350552325-0.0985759841408-0.0192927938676-0.39922811679-0.2952721348030.1397176736390.1851407772290.0304002449786-0.492996465899-0.1119726615910.437252190365-0.00712240804336-0.1420459214160.320646080739-0.1299465438550.462533798302-29.6797754837-48.1000704501-75.9131793482
212.91239741294-0.572958604784-0.2584809208210.8130170295620.1197914327930.7855915655750.14705192830.324430663435-0.410989007897-0.088285447487-0.119539209963-0.05975416418920.2161546885030.0573249817671-0.01376143986530.2939285465570.0787938785442-0.04944410244760.214807507083-0.06084299960290.300692960429-6.4121957251-43.5265931865-71.7300320111
221.132138508632.03102746863-0.689700407374.581978936990.2906061493093.46049857641-0.1582993392660.0263978686140.239308418873-0.3789048691260.1047226831810.49319200435-0.192986699426-0.401466581471-0.01422467689090.4474981628760.163410440806-0.07730823720890.4085610309740.01758969350030.286468173573-34.7839730561-1.12138575111-87.6659470717
233.99514159796-0.4528575410110.1529427652842.14381378206-0.01922561939091.068072348650.0421765958740.1260780780420.107655925342-0.23337391456-0.0747102145469-0.0553886194479-0.04050842392030.1285536745110.01898588324650.353398963210.0907773334505-0.003943893076410.310874902066-0.008916602135330.128726731461-14.7825285929-15.4279257654-89.2341044008
244.612131648485.87677736803-2.688079789738.91309270286-4.885224017323.045947267710.1578560212550.008398323957070.2166472998110.395590146912-0.1534357893710.150017158109-0.3785162606510.06217484692610.04692940312030.3493515472030.1143658140060.007804247024480.398786092353-0.04672569727690.24811671829-12.2243726049-23.7061824102-81.9666082887
251.5784898423-0.1745480472330.3879975951720.8708107411360.1722515431591.938446658970.1669744033920.489662335832-0.00386462681598-0.452293280078-0.120554260544-0.0543486511934-0.1196554589820.162104753644-0.04150076345540.4602855214040.1132703460590.02889330799590.448302697492-0.004985257634040.18646944308-17.4069039665-16.6385363353-100.100926904
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 116 )AA12 - 1161 - 105
22chain 'A' and (resid 117 through 159 )AA117 - 159106 - 148
33chain 'A' and (resid 160 through 249 )AA160 - 249149 - 238
44chain 'B' and (resid 12 through 59 )BB12 - 591 - 48
55chain 'B' and (resid 60 through 250 )BB60 - 25049 - 239
66chain 'C' and (resid 12 through 38 )CD12 - 381 - 27
77chain 'C' and (resid 39 through 159 )CD39 - 15928 - 130
88chain 'C' and (resid 160 through 187 )CD160 - 187131 - 158
99chain 'C' and (resid 188 through 250 )CD188 - 250159 - 221
1010chain 'D' and (resid 12 through 38 )DC12 - 381 - 27
1111chain 'D' and (resid 39 through 59 )DC39 - 5928 - 43
1212chain 'D' and (resid 60 through 135 )DC60 - 13544 - 119
1313chain 'D' and (resid 136 through 159 )DC136 - 159120 - 132
1414chain 'D' and (resid 160 through 187 )DC160 - 187133 - 160
1515chain 'D' and (resid 188 through 205 )DC188 - 205161 - 178
1616chain 'D' and (resid 206 through 234 )DC206 - 234179 - 207
1717chain 'D' and (resid 235 through 250 )DC235 - 250208 - 223
1818chain 'E' and (resid 12 through 72 )EE12 - 721 - 61
1919chain 'E' and (resid 73 through 135 )EE73 - 13562 - 124
2020chain 'E' and (resid 136 through 159 )EE136 - 159125 - 148
2121chain 'E' and (resid 160 through 250 )EE160 - 250149 - 239
2222chain 'F' and (resid 5 through 35 )FF5 - 351 - 31
2323chain 'F' and (resid 36 through 87 )FF36 - 8732 - 73
2424chain 'F' and (resid 88 through 101 )FF88 - 10174 - 87
2525chain 'F' and (resid 102 through 250 )FF102 - 25088 - 226

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