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- PDB-6jw4: Degenerate RVD RG forms a distinct loop conformation -

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Basic information

Entry
Database: PDB / ID: 6jw4
TitleDegenerate RVD RG forms a distinct loop conformation
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
  • TAL effector
KeywordsDNA BINDING PROTEIN/DNA / methylation TAL effector complex / DNA BINDING PROTEIN-DNA complex
Function / homologyTAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsLiu, L. / Yi, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953201 China
National Natural Science Foundation of China (NSFC)21825701 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.
Authors: Liu, L. / Zhang, Y. / Liu, M. / Wei, W. / Yi, C. / Peng, J.
History
DepositionApr 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAL effector
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
B: TAL effector
C: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
E: TAL effector
F: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
G: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
H: TAL effector
K: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
L: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)249,31012
Polymers249,31012
Non-polymers00
Water00
1
A: TAL effector
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3273
Polymers62,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-54 kcal/mol
Surface area24730 Å2
MethodPISA
2
B: TAL effector
C: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3273
Polymers62,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-53 kcal/mol
Surface area24690 Å2
MethodPISA
3
E: TAL effector
F: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
G: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3273
Polymers62,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-54 kcal/mol
Surface area24650 Å2
MethodPISA
4
H: TAL effector
K: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
L: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3273
Polymers62,3273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-55 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.050, 93.971, 167.686
Angle α, β, γ (deg.)90.000, 102.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23H
14I
24C
15I
25F
16I
26K
17J
27D
18J
28G
19J
29L
110B
210E
111B
211H
112C
212F
113C
213K
114D
214G
115D
215L
116E
216H
117F
217K
118G
218L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA230 - 7211 - 492
21METMETLEULEUBD230 - 7211 - 492
12METMETLEULEUAA230 - 7211 - 492
22METMETLEULEUEG230 - 7211 - 492
13METMETLEULEUAA230 - 7211 - 492
23METMETLEULEUHJ230 - 7211 - 492
14DTDTDTDTIB-2 - 141 - 17
24DTDTDTDTCE-2 - 141 - 17
15DTDTDTDTIB-2 - 141 - 17
25DTDTDTDTFH-2 - 141 - 17
16DTDTDTDTIB-2 - 141 - 17
26DTDTDTDTKK-2 - 141 - 17
17DADADADAJC-14 - 21 - 17
27DADADADADF-14 - 21 - 17
18DADADADAJC-14 - 21 - 17
28DADADADAGI-14 - 21 - 17
19DADADADAJC-14 - 21 - 17
29DADADADALL-14 - 21 - 17
110METMETLEULEUBD230 - 7211 - 492
210METMETLEULEUEG230 - 7211 - 492
111METMETLEULEUBD230 - 7211 - 492
211METMETLEULEUHJ230 - 7211 - 492
112DTDTDTDTCE-2 - 141 - 17
212DTDTDTDTFH-2 - 141 - 17
113DTDTDTDTCE-2 - 141 - 17
213DTDTDTDTKK-2 - 141 - 17
114DADADADADF-14 - 21 - 17
214DADADADAGI-14 - 21 - 17
115DADADADADF-14 - 21 - 17
215DADADADALL-14 - 21 - 17
116METMETLEULEUEG230 - 7211 - 492
216METMETLEULEUHJ230 - 7211 - 492
117DTDTDTDTFH-2 - 141 - 17
217DTDTDTDTKK-2 - 141 - 17
118DADADADAGI-14 - 21 - 17
218DADADADALL-14 - 21 - 17

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
TAL effector


Mass: 51881.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72*PLUS
#2: DNA chain
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3')


Mass: 5126.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5319.477 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 8-10% PEG3350 (w/v), 10% ethanol and 0.1M MES pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.09→163.51 Å / Num. obs: 43409 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rrim(I) all: 0.107 / Net I/σ(I): 2.05
Reflection shellResolution: 3.09→3.21 Å / Num. unique obs: 43409 / Rrim(I) all: 0.107

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GJP
Resolution: 3.09→163.51 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.868 / SU B: 42 / SU ML: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.567
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 2320 5.1 %RANDOM
Rwork0.2434 ---
obs0.2449 43409 86.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 227.11 Å2 / Biso mean: 70 Å2 / Biso min: 27.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å23.86 Å2
2---2.36 Å20 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 3.09→163.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14268 2768 0 0 17036
Num. residues----2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01817572
X-RAY DIFFRACTIONr_bond_other_d0.0040.0216272
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.83124532
X-RAY DIFFRACTIONr_angle_other_deg1.115337392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22451964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60625.821536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.438152368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711572
X-RAY DIFFRACTIONr_chiral_restr0.0720.22860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118432
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023680
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A308280.05
12B308280.05
21A307910.04
22E307910.04
31A306610.05
32H306610.05
41I14130.07
42C14130.07
51I13990.06
52F13990.06
61I13540.12
62K13540.12
71J12980.02
72D12980.02
81J12820.04
82G12820.04
91J12980.03
92L12980.03
101B307020.05
102E307020.05
111B305800.06
112H305800.06
121C14040.07
122F14040.07
131C13490.12
132K13490.12
141D12780.05
142G12780.05
151D12920.03
152L12920.03
161E306520.06
162H306520.06
171F13530.11
172K13530.11
181G12770.05
182L12770.05
LS refinement shellResolution: 3.09→3.169 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.448 68 -
Rwork0.368 1330 -
obs--36.26 %
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)
12.00090.48240.32223.6480.64544.0149-0.2190.09350.0835-0.23490.27220.0006-0.0863-0.1744-0.05320.1417-0.0161-0.15580.38780.04130.2119-1.0140.364922.8157
22.7951-0.9773-1.44543.6702-2.59833.7123-0.0087-0.38570.1171-0.3090.06570.00780.23150.4796-0.0570.2364-0.18-0.10520.5307-0.09330.15850.9162-3.540517.6093
33.8940.14842.14863.3991.68686.53020.26820.07610.1016-0.64960.0898-0.6178-0.6357-0.0984-0.35790.451-0.1626-0.010.3664-0.020.25792.7528-2.787416.3981
41.56950.6763-0.55573.1536-1.25652.6090.0374-0.1001-0.09840.5879-0.1277-0.1358-0.43330.4670.09040.373-0.0569-0.22560.3866-0.00540.2447-20.928947.075860.6992
54.19851.7394-2.65534.26721.1383.11490.38880.0556-0.15880.5143-0.3721-0.2376-0.1589-0.2506-0.01670.539-0.1045-0.17020.22120.11520.1479-23.059543.146865.6305
63.8681-0.40350.20643.9792-1.24715.23440.0514-0.1470.10230.84590.01670.4142-1.14690.0715-0.06810.64560.0132-0.06590.23290.05830.2711-25.186343.849466.6826
73.3871-1.7245-1.53172.57220.85012.94760.37710.4081-0.1872-0.6427-0.6526-0.1445-0.00350.00990.27550.56680.1345-0.16710.5364-0.05370.4329.9651-7.401660.9532
81.4969-2.8839-1.53778.001-0.25155.85730.3811-0.0402-0.1122-0.9778-0.40420.2129-0.10260.6080.02310.48660.199-0.07790.5164-0.19110.391935.7377-10.229958.3306
97.5519-1.0489-1.52424.80891.27045.2957-0.47290.3738-0.4657-0.62320.1244-0.2723-0.00240.05750.34850.6870.2048-0.04050.37710.1440.436935.4151-12.559557.795
103.29240.71660.26881.9239-0.3263.60120.06290.1214-0.00240.0112-0.25580.07110.43250.01530.19290.35570.0794-0.16210.4243-0.03590.315746.25440.201319.2269
110.49540.3522-1.68966.3731-0.60276.0676-0.08520.1388-0.0552-0.2404-0.0590.50840.6354-0.48460.14410.3139-0.0904-0.14140.4119-0.03490.202140.108437.155121.1022
129.4354-0.19382.26354.0013-0.10172.9391-0.4399-0.2996-0.41190.38440.1760.21080.5094-0.16660.26380.4552-0.1086-0.07870.5178-0.05350.379940.348235.027421.5987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A230 - 721
2X-RAY DIFFRACTION2I-2 - 14
3X-RAY DIFFRACTION3J-14 - 2
4X-RAY DIFFRACTION4B230 - 721
5X-RAY DIFFRACTION5C-2 - 14
6X-RAY DIFFRACTION6D-14 - 2
7X-RAY DIFFRACTION7E230 - 721
8X-RAY DIFFRACTION8F-2 - 14
9X-RAY DIFFRACTION9G-14 - 2
10X-RAY DIFFRACTION10H230 - 721
11X-RAY DIFFRACTION11K-2 - 14
12X-RAY DIFFRACTION12L-14 - 2

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