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- PDB-5xvn: E. far Cas1-Cas2/prespacer binary complex -

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Basic information

Entry
Database: PDB / ID: 5xvn
TitleE. far Cas1-Cas2/prespacer binary complex
Components
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2
  • DNA (28-MER)
KeywordsIMMUNE SYSTEM / CRISPR / Cas
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, NMENI subtype / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesEnterococcus faecalis TX0027 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.25 Å
AuthorsXiao, Y. / Ng, S. / Nam, K.H. / Ke, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
CitationJournal: Nature / Year: 2017
Title: How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration.
Authors: Xiao, Y. / Ng, S. / Hyun Nam, K. / Ke, A.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 12, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (28-MER)
H: DNA (28-MER)
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2
N: CRISPR-associated endoribonuclease Cas2
O: DNA (28-MER)
P: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,14020
Polymers354,04316
Non-polymers974
Water362
1
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (28-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,07010
Polymers177,0228
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23510 Å2
ΔGint-162 kcal/mol
Surface area62550 Å2
MethodPISA
2
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2
N: CRISPR-associated endoribonuclease Cas2
O: DNA (28-MER)
P: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,07010
Polymers177,0228
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23560 Å2
ΔGint-156 kcal/mol
Surface area63090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.711, 160.711, 187.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24I
15A
25J
16A
26K
17A
27L
18B
28C
19B
29D
110B
210I
111B
211J
112B
212K
113B
213L
114C
214D
115C
215I
116C
216J
117C
217K
118C
218L
119D
219I
120D
220J
121D
221K
122D
222L
123E
223F
124E
224M
125E
225N
126F
226M
127F
227N
128G
228H
129G
229O
130G
230P
131H
231O
132H
232P
133I
233J
134I
234K
135I
235L
136J
236K
137J
237L
138K
238L
139M
239N
140O
240P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 288
2010B1 - 288
1020A1 - 288
2020C1 - 288
1030A2 - 288
2030D2 - 288
1040A1 - 288
2040I1 - 288
1050A1 - 288
2050J1 - 288
1060A1 - 288
2060K1 - 288
1070A1 - 288
2070L1 - 288
1080B1 - 288
2080C1 - 288
1090B2 - 288
2090D2 - 288
10100B1 - 288
20100I1 - 288
10110B1 - 288
20110J1 - 288
10120B1 - 288
20120K1 - 288
10130B1 - 288
20130L1 - 288
10140C2 - 288
20140D2 - 288
10150C1 - 288
20150I1 - 288
10160C1 - 288
20160J1 - 288
10170C1 - 288
20170K1 - 288
10180C1 - 288
20180L1 - 288
10190D2 - 288
20190I2 - 288
10200D2 - 288
20200J2 - 288
10210D2 - 288
20210K2 - 288
10220D2 - 288
20220L2 - 288
10230E5 - 107
20230F5 - 107
10240E5 - 107
20240M5 - 107
10250E5 - 108
20250N5 - 108
10260F1 - 108
20260M1 - 108
10270F5 - 107
20270N5 - 107
10280G2 - 24
20280H2 - 24
10290G2 - 25
20290O2 - 25
10300G2 - 24
20300P2 - 24
10310H2 - 24
20310O2 - 24
10320H2 - 25
20320P2 - 25
10330I1 - 288
20330J1 - 288
10340I1 - 288
20340K1 - 288
10350I1 - 288
20350L1 - 288
10360J1 - 288
20360K1 - 288
10370J1 - 288
20370L1 - 288
10380K1 - 288
20380L1 - 288
10390M5 - 107
20390N5 - 107
10400O2 - 24
20400P2 - 24

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40

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Components

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 33492.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas1, HMPREF9501_02814 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD7, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endoribonuclease Cas2


Mass: 12977.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria)
Gene: cas2, HMPREF9501_02813 / Production host: Escherichia coli (E. coli)
References: UniProt: E6GPD6, Hydrolases; Acting on ester bonds
#3: DNA chain
DNA (28-MER)


Mass: 8548.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl, pH 8.5, and 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.25→49.41 Å / Num. obs: 71385 / % possible obs: 100 % / Redundancy: 7.1 % / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 3.25→49.41 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU B: 24.386 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24907 3714 5 %RANDOM
Rwork0.20593 ---
obs0.20805 71255 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.085 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 3.25→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22060 2023 4 2 24089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01924779
X-RAY DIFFRACTIONr_bond_other_d0.0070.0223235
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.87833821
X-RAY DIFFRACTIONr_angle_other_deg1.497353279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27652670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17723.861127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.898154237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.82115166
X-RAY DIFFRACTIONr_chiral_restr0.0840.23676
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226407
X-RAY DIFFRACTIONr_gen_planes_other0.0060.026009
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6878.29910731
X-RAY DIFFRACTIONr_mcbond_other5.6878.29910730
X-RAY DIFFRACTIONr_mcangle_it8.81612.45113384
X-RAY DIFFRACTIONr_mcangle_other8.81612.45113385
X-RAY DIFFRACTIONr_scbond_it5.8368.68914048
X-RAY DIFFRACTIONr_scbond_other5.8368.68814047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.13712.87320438
X-RAY DIFFRACTIONr_long_range_B_refined13.23968.10829033
X-RAY DIFFRACTIONr_long_range_B_other13.2468.10629032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170810.14
12B170810.14
21A179320.11
22C179320.11
31A147810.14
32D147810.14
41A182850.1
42I182850.1
51A170190.13
52J170190.13
61A178920.11
62K178920.11
71A173520.13
72L173520.13
81B170190.13
82C170190.13
91B151870.14
92D151870.14
101B170150.13
102I170150.13
111B183080.11
112J183080.11
121B169820.14
122K169820.14
131B177400.12
132L177400.12
141C149240.14
142D149240.14
151C180350.1
152I180350.1
161C172070.13
162J172070.13
171C184660.09
172K184660.09
181C173420.12
182L173420.12
191D148230.14
192I148230.14
201D155350.14
202J155350.14
211D148680.14
212K148680.14
221D157380.12
222L157380.12
231E56310.16
232F56310.16
241E58390.12
242M58390.12
251E56580.16
252N56580.16
261F58210.16
262M58210.16
271F59060.13
272N59060.13
281G18840.04
282H18840.04
291G19490.05
292O19490.05
301G18900.02
302P18900.02
311H18880.02
312O18880.02
321H19570.06
322P19570.06
331I171130.13
332J171130.13
341I181710.1
342K181710.1
351I173780.12
352L173780.12
361J171200.13
362K171200.13
371J178670.12
372L178670.12
381K172750.13
382L172750.13
391M54940.17
392N54940.17
401O18880.03
402P18880.03
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 231 -
Rwork0.359 5258 -
obs--99.95 %

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