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- PDB-8q3y: Crystal structure of apo Can2 from Thermoanaerobacter brockii -

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Basic information

Entry
Database: PDB / ID: 8q3y
TitleCrystal structure of apo Can2 from Thermoanaerobacter brockii
ComponentsDUF1887 family protein
KeywordsDNA BINDING PROTEIN / Can2 / CARF / CRISPR-Cas
Function / homologytRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / DUF1887 family protein
Function and homology information
Biological speciesThermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsJungfer, K. / Sigg, A. / Jinek, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820152European Union
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.
Authors: Jungfer, K. / Sigg, A. / Jinek, M.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF1887 family protein
B: DUF1887 family protein


Theoretical massNumber of molelcules
Total (without water)102,8012
Polymers102,8012
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.427, 79.956, 94.060
Angle α, β, γ (deg.)90.000, 92.970, 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 DUF1887 family protein


Mass: 51400.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
Gene: Thebr_0943 / Production host: Escherichia coli (E. coli) / References: UniProt: E8URK0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.37 Å3/Da / Density % sol: 48.1 % / Description: plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris pH 8, 17.1% (v/v) PEG 550 MME, 4.3% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→49.16 Å / Num. obs: 30882 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 44.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09674 / Rpim(I) all: 0.03928 / Rrim(I) all: 0.1045 / Net I/σ(I): 14.25
Reflection shellResolution: 2.523→2.613 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.7153 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 3041 / CC1/2: 0.831 / Rrim(I) all: 0.7707 / % possible all: 98.16

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROC20230726data scaling
XDS20220110data reduction
Coot0.9.8.9model building
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→49.16 Å / SU ML: 0.3206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 1516 4.91 %
Rwork0.1896 29360 -
obs0.1917 30876 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.69 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7214 0 0 16 7230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00397368
X-RAY DIFFRACTIONf_angle_d0.64079908
X-RAY DIFFRACTIONf_chiral_restr0.04511072
X-RAY DIFFRACTIONf_plane_restr0.0041250
X-RAY DIFFRACTIONf_dihedral_angle_d12.42912794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.60.30361440.24672652X-RAY DIFFRACTION98.17
2.6-2.70.34691570.2492590X-RAY DIFFRACTION98.25
2.7-2.810.28021460.25832620X-RAY DIFFRACTION98.29
2.81-2.930.31851060.23522685X-RAY DIFFRACTION98.55
2.93-3.090.31380.23652682X-RAY DIFFRACTION98.67
3.09-3.280.28591410.24582629X-RAY DIFFRACTION98.68
3.28-3.530.28451090.22942693X-RAY DIFFRACTION99.01
3.53-3.890.22991490.18292682X-RAY DIFFRACTION98.95
3.89-4.450.17411550.1522670X-RAY DIFFRACTION99.12
4.45-5.610.17841170.14582722X-RAY DIFFRACTION99.27
5.61-49.160.17951540.15042735X-RAY DIFFRACTION98.9
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)
10.939315651009-0.575393265425-0.3712643945730.851175172808-0.5635875523251.41286589234-0.00900900782807-0.0729482407229-0.07307037296780.180192605141-0.149894757229-0.2138892590050.07334677069210.416069750093-1.21977423435E-70.375299979256-0.00798574885538-0.04726413219530.4167161490540.08172177932120.36328256894734.0337381884-5.5894681665646.6207739917
21.0764783493-0.511261630598-0.4911869710910.7108587275340.1595965030.4572552915330.0204769171625-0.352246391252-0.02203068470840.269734399021-0.08468956792440.3547211111610.02776706675690.0814509067967-0.0004757708853230.459515449603-0.0290899802743-0.001261701725120.3980206404850.02239309202340.34868444218824.8635134326-0.199482676354.3534792613
30.1251419465920.2011589609370.05589090583240.38030302915-0.06521339953430.3335654015560.1004414717650.05409655856850.1076501510130.299232626773-0.0668542372795-0.4189766829430.04572309860410.4972798500790.01031895931250.3538137547930.0215680317616-0.04363208907350.44273904190.08141995322180.44141189302538.62568709421.3344628281426.7248337154
42.02153285318-0.31606610218-0.5275652868351.68506607978-0.5199799287071.60815503183-0.009176902499290.0973790153793-0.16678863451-0.06012561402160.0750017518249-0.0273267730860.0124598879618-0.0239209763363.18153389295E-90.248582161904-0.003891337842150.001826167429760.23543491992-0.001926467680470.27119168784133.70398758451.60904359575-8.08450479316
51.111323527140.340498463305-0.2145962509161.10877826242-0.129900994961.657066147840.0204554280477-0.004492946853830.00198268986940.0415056872836-0.119792991693-0.0136533408489-0.186090158222-0.08968888129535.4399409284E-90.2389113623220.02582358658410.03412703779730.2078032523540.02323315176750.24567594687427.04703595083.8355063598118.7135390423
60.154908780656-0.1547906729820.06703291536460.293693937496-0.1209618864750.0927271503275-0.0775257674686-0.1173857890630.3387262139450.153270054040.02353262172970.139543449798-0.56145010828-0.165115923806-0.0004002175511660.4804085941770.07048480092220.001915551979690.349864409786-2.99444142169E-50.36994870703723.186870821813.023004481618.825605709
71.5851826224-0.3313428920320.8862613352710.705684982335-0.5737828993052.09947115563-0.0762616122158-0.5272900652880.2101440196630.182177296517-0.0711659036642-0.0147624662333-0.272445546684-0.455248205549-0.01467507918920.3263245151930.001489159451120.05682780597960.597534350272-0.06839075937210.3414579091693.9675825265-1.2195205171750.9809586944
80.5488218472720.05324384626620.8712030073820.5915358832890.1923896417652.000116548530.0381004764055-0.0578346761447-0.0530667445754-0.035086267521-0.1075344483720.02985519452530.10423655058-0.353638684037-0.001052001863850.290037757439-0.04761595682910.01497382648780.3469080997920.04622152419140.401681491463-3.38858927147-14.315150716911.3694176204
90.395246369190.04864742046550.1397230674970.00451385358430.0151212368330.04612528580140.2925057140660.3396006760090.286541634262-0.244587378803-0.158612704862-0.550259459579-0.1936253688510.2866528952930.001932378213990.548869069908-0.00412073096070.116209746470.5613365057820.1399283655010.5764179476054.26210809366-11.8234879477-14.5498650327
101.225962677420.2164816042090.4280580667540.6495062714030.1661194777920.4126847696870.1284012840270.00458940063243-0.00919483924438-0.190234258216-0.04364276554450.1180188169090.054007828818-0.2834127997470.02149073122530.283204519221-0.0717894374073-0.01890421461710.2602597205740.03468795014950.410416810723-6.1116207926-16.04624506444.82604267598
110.9247439883490.6697199787580.5921818418870.8206637001010.06064295321290.8733993268680.103306268555-0.1218389639520.0272837644170.07492537256830.00226854128693-0.1315255063680.09634918301670.185271528624-5.88521239589E-80.2563624703690.0129886950798-0.0004816750909580.262205573621-0.007518256879170.3008264976079.48063159107-15.121515305521.7102172424
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 69 )AA2 - 691 - 68
22chain 'A' and (resid 70 through 146 )AA70 - 14669 - 145
33chain 'A' and (resid 147 through 175 )AA147 - 175146 - 174
44chain 'A' and (resid 176 through 298 )AA176 - 298175 - 297
55chain 'A' and (resid 299 through 409 )AA299 - 409298 - 408
66chain 'A' and (resid 410 through 437 )AA410 - 437409 - 436
77chain 'B' and (resid 2 through 146 )BB2 - 1461 - 145
88chain 'B' and (resid 147 through 225 )BB147 - 225146 - 224
99chain 'B' and (resid 226 through 253 )BB226 - 253225 - 252
1010chain 'B' and (resid 254 through 333 )BB254 - 333253 - 332
1111chain 'B' and (resid 334 through 437 )BB334 - 437333 - 436

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