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- PDB-5zyf: Crystal structure of Streptococcus pyogenes type II-A Cas2 -

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Basic information

Entry
Database: PDB / ID: 5zyf
TitleCrystal structure of Streptococcus pyogenes type II-A Cas2
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsPROTEIN BINDING / CRISPR / Cas2 / CRISPR-associated / Streptococcus pyogenes
Function / homologyCRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding / CRISPR-associated endoribonuclease Cas2
Function and homology information
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsKa, D. / Bae, E.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1D1A1A09916821 Korea, Republic Of
Rural Development AdministrationPJ013181 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2
Authors: Ka, D. / Jang, D.M. / Han, B.W. / Bae, E.
History
DepositionMay 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
A: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
C: CRISPR-associated endoribonuclease Cas2
D: CRISPR-associated endoribonuclease Cas2
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,01321
Polymers63,8786
Non-polymers1,13515
Water5,260292
1
A: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,91911
Polymers21,2932
Non-polymers6279
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-27 kcal/mol
Surface area9930 Å2
MethodPISA
2
C: CRISPR-associated endoribonuclease Cas2
D: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6776
Polymers21,2932
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-53 kcal/mol
Surface area10290 Å2
MethodPISA
3
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4174
Polymers21,2932
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-11 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.771, 75.292, 145.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CRISPR-associated endoribonuclease Cas2 / Cas2 protomer Chain A


Mass: 10646.388 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas2, SPy_1048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99ZW0, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 22.0% (w/v) PEG 4000, 325 mM ammonium sulfate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 56417 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 1.012 / Net I/σ(I): 22.45
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.417 / Num. unique obs: 5499 / CC1/2: 0.903 / Rpim(I) all: 0.228 / Rrim(I) all: 0.594 / Χ2: 1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
PHENIXmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.76→36.448 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.2336 2000 3.55 %
Rwork0.1971 --
obs0.1984 56344 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→36.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 66 292 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084261
X-RAY DIFFRACTIONf_angle_d1.0185661
X-RAY DIFFRACTIONf_dihedral_angle_d13.6381645
X-RAY DIFFRACTIONf_chiral_restr0.045603
X-RAY DIFFRACTIONf_plane_restr0.005704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7569-1.80080.31191370.2693704X-RAY DIFFRACTION97
1.8008-1.84950.33351410.25633840X-RAY DIFFRACTION100
1.8495-1.90390.29071400.23333810X-RAY DIFFRACTION100
1.9039-1.96540.23321420.20443858X-RAY DIFFRACTION100
1.9654-2.03560.21931430.20413880X-RAY DIFFRACTION100
2.0356-2.11710.22281420.20813856X-RAY DIFFRACTION100
2.1171-2.21340.22131420.19463872X-RAY DIFFRACTION100
2.2134-2.33010.24231420.19773853X-RAY DIFFRACTION100
2.3301-2.47610.25781420.20123865X-RAY DIFFRACTION100
2.4761-2.66720.24461440.20273899X-RAY DIFFRACTION100
2.6672-2.93550.2481440.21243908X-RAY DIFFRACTION100
2.9355-3.360.25891440.19793941X-RAY DIFFRACTION100
3.36-4.23220.20871470.17943973X-RAY DIFFRACTION100
4.2322-36.45550.20821500.18314085X-RAY DIFFRACTION99
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)
14.1853-1.84620.30237.6704-0.32484.9310.1430.250.2797-0.0035-0.2521-0.026-0.4289-0.29930.0570.15990.00820.00940.22320.0280.15797.43626.5858112.3322
23.1635-2.29070.13137.97970.05352.92120.0990.3738-0.417-0.2015-0.03990.55130.1881-0.2957-0.01320.1066-0.0378-0.01440.2490.02450.22347.956111.8666110.6948
35.9961-1.2801-4.99566.71190.61964.18240.07060.1582-0.0224-0.61880.1284-0.01280.0317-0.2478-0.11640.25510.0531-0.02180.2760.04640.16447.769223.5509104.859
41.4364-1.2438-2.13883.34361.79063.4429-0.0254-0.29790.20760.23330.45771.0739-0.2158-1.11850.35970.23580.20610.13160.53570.12090.4786-0.759830.0454112.723
56.8808-5.2855-1.49015.14782.51152.06410.2305-0.4238-0.33740.64060.02060.6899-0.3863-0.7176-0.04620.25290.06680.14420.4010.06250.26931.070522.8934120.4865
61.5747-0.46021.18683.8303-4.24295.1858-0.07360.04270.08650.8533-0.0354-0.2949-0.3442-0.12850.04810.07440.00370.00630.19450.02370.165610.429624.3414116.2584
78.9289-1.7172-1.78686.10983.37187.24660.51770.60760.4126-0.3523-0.150.3290.2161-0.3402-0.35710.29560.09350.0010.2780.09490.26896.974739.6649105.6855
83.3229-3.50542.74863.8256-2.86233.07180.05030.3857-0.8068-0.68450.10410.77060.5248-0.1473-0.12480.30530.02920.01240.2393-0.01870.316818.035928.372899.9217
95.028-3.6742-1.36892.50870.72371.3423-0.0067-0.0834-0.23930.16690.02550.1111-0.0647-0.0209-0.03410.17490.00820.00090.14170.00430.148920.642126.786110.0725
104.57022.83280.12137.97291.74833.37540.0044-0.0678-0.22510.17860.0552-0.3787-0.02380.2706-0.08490.1538-0.0003-0.00350.2241-0.00790.244130.146124.5168109.3899
112.0638-0.18480.47999.049-3.99323.1865-0.0223-0.05260.16410.21540.0022-0.2578-0.11590.08350.04910.1384-0.0099-0.0340.1816-0.02390.195523.070835.2459113.4197
124.34530.0155-0.81126.0572-3.66022.8597-0.04930.3888-0.1423-0.2398-0.0799-0.32130.09120.10810.1510.1494-0.03260.00410.2248-0.03280.154425.238732.6335100.9841
131.2612-0.2688-0.54215.7793-1.57562.10070.0471-0.15260.06120.69730.21650.1567-0.3096-0.1537-0.25860.18850.01780.00170.1894-0.00420.146513.223332.0398117.3811
144.81853.8639-2.82054.2341-2.70165.12830.28030.3048-0.09310.3386-0.18810.24320.15490.2048-0.01910.31870.0322-0.01450.2565-0.02420.2443-2.642637.816487.52
156.7993.9555-2.1842.6065-1.73864.42660.17820.6417-0.4876-0.4709-0.06970.84940.6704-0.352-0.12420.34470.0162-0.120.3428-0.09980.5403-15.830232.018487.0366
166.5685-1.7442-2.74936.65220.92162.54760.08910.80240.0556-0.1183-0.2090.30680.1667-0.74780.19330.2960.0136-0.01750.40570.01790.2155-4.193140.842383.0583
176.60280.10390.08586.84520.77017.5648-0.0734-0.345-0.188-0.16090.31080.75510.0073-0.128-0.09070.14970.03760.02070.242-0.01590.2425-10.869639.463795.2965
182.6071.7997-2.6786.4511-0.6116.0879-0.05310.35460.1506-0.88790.008-0.1116-0.66780.40980.0310.3038-0.0202-0.01220.30880.04280.17815.679841.552585.0046
197.01962.6376-0.38764.5046-1.34975.95540.25160.5397-0.4398-1.40450.2150.4420.28630.2111-0.38490.36570.0358-0.04270.3265-0.03950.22644.98928.362879.1993
203.74780.8056-0.47447.0484-1.27674.38450.3548-0.693-0.6073-0.3318-0.40080.05610.0869-0.57850.03490.2154-0.057-0.09560.37250.06780.25396.097528.149489.8651
218.67964.11180.55219.02351.5716.27410.0386-0.5248-1.25380.03910.04250.25991.4333-0.3688-0.16110.4439-0.0502-0.04650.27270.09870.39346.315416.685891.4047
224.6115-1.80424.13134.03210.20664.7707-0.1831-0.39820.13520.140.05410.1295-0.271-0.18020.15140.1978-0.0205-0.02530.28460.04320.21349.663528.924893.6903
230.7567-1.08970.88968.15380.20344.50670.46310.3708-0.0718-1.5518-0.47080.16551.62350.4881-0.25190.58620.1053-0.03580.4177-0.03470.2769.598221.338182.1755
243.22660.78920.46042.4542.74667.81850.03750.06240.156-0.0463-0.0177-0.08-0.47430.29830.01520.2079-0.0101-0.03090.27030.04060.17399.190938.860991.4533
254.83324.8074-2.61934.7414-2.6062.55060.0571-0.6839-0.29360.19190.11370.20510.54980.19050.00570.29040.03770.03640.3729-0.01690.2834-4.253235.546298.1082
261.0109-0.89742.02254.3068-1.51993.93030.1188-0.75470.06960.84910.20591.35-0.3989-0.6428-0.10980.4860.04040.24860.43040.04030.5368-3.307150.636456.6272
272.7754-3.7839-2.09725.26342.67713.33610.1489-0.4617-0.00520.5328-0.30930.0507-0.5649-0.0726-0.19850.4482-0.090.03290.3240.00590.18346.421647.556456.0209
282.96441.5443-0.94684.4501-2.05924.66370.7149-0.34820.11590.5565-0.4599-0.199-0.56250.08880.53670.7323-0.04640.20570.4-0.05770.18155.148645.330960.9288
291.95091.07763.12115.8665-0.80957.0409-0.2010.27340.2004-0.4188-0.41710.72330.07510.30850.58740.51680.0223-0.00660.3274-0.07060.31-2.134935.060264.8775
303.4524-2.10322.97297.4142-0.67963.06720.3966-0.3408-0.7921.568-0.38180.93750.8951-0.38550.03980.7345-0.25830.03030.4702-0.05970.4757-7.865828.869.8383
316.26296.03420.98378.02092.88713.25050.91020.0689-0.4172-0.8084-0.7551.0645-0.2745-1.4862-0.38560.64220.1163-0.11280.50050.02490.3094-1.427237.217171.0127
321.97130.78440.94998.56162.67342.30380.2274-0.2982-0.376-1.1751-0.1581-0.22160.80870.8133-0.03840.4690.09340.03310.51880.06150.22425.699931.223171.1513
330.18370.10240.62940.04820.31382.0542-1.0981-0.7349-0.89660.5256-0.1079-0.43910.25270.76520.01860.94380.21630.23790.96390.08261.079111.782222.529664.8505
346.8251.2492-0.54922.2114-1.36248.0991-0.53340.7749-0.7162-1.350.4370.83321.5385-0.55990.18910.7044-0.1686-0.09310.38-0.02420.3423-3.109526.074860.4246
352.56281.39340.09856.23260.48336.4371-0.1303-0.9393-0.00610.3186-0.5191-0.1803-0.13371.7549-0.39470.5488-0.1226-0.04990.91270.1530.117410.854438.334467.8251
362.518-2.20843.25246.4262-2.75534.24820.3197-0.8745-0.14711.1690.03291.055-0.3123-1.6329-0.42011.104-0.16860.31790.7425-0.04630.39851.467649.010369.443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 66 )
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 78 )
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 84 )
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 91 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 35 )
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 52 )
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 92 )
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 14 )
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 35 )
16X-RAY DIFFRACTION16chain 'C' and (resid 36 through 55 )
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 71 )
18X-RAY DIFFRACTION18chain 'C' and (resid 72 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 90 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 19 )
21X-RAY DIFFRACTION21chain 'D' and (resid 20 through 35 )
22X-RAY DIFFRACTION22chain 'D' and (resid 36 through 57 )
23X-RAY DIFFRACTION23chain 'D' and (resid 58 through 71 )
24X-RAY DIFFRACTION24chain 'D' and (resid 72 through 84 )
25X-RAY DIFFRACTION25chain 'D' and (resid 85 through 92 )
26X-RAY DIFFRACTION26chain 'E' and (resid 7 through 35 )
27X-RAY DIFFRACTION27chain 'E' and (resid 36 through 57 )
28X-RAY DIFFRACTION28chain 'E' and (resid 58 through 90 )
29X-RAY DIFFRACTION29chain 'F' and (resid 6 through 22 )
30X-RAY DIFFRACTION30chain 'F' and (resid 23 through 36 )
31X-RAY DIFFRACTION31chain 'F' and (resid 37 through 44 )
32X-RAY DIFFRACTION32chain 'F' and (resid 45 through 49 )
33X-RAY DIFFRACTION33chain 'F' and (resid 50 through 56 )
34X-RAY DIFFRACTION34chain 'F' and (resid 57 through 71 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 84 )
36X-RAY DIFFRACTION36chain 'F' and (resid 85 through 90 )

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