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- PDB-6jw3: Degenerate RVD RG forms a distinct loop conformation -

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Basic information

Entry
Database: PDB / ID: 6jw3
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*(5CM)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 / homology: / TAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLiu, L. / Yi, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21825701 China
National Natural Science Foundation of China91740112 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*(5CM)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*(5CM)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*(5CM)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*(5CM)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)249,24612
Polymers249,24612
Non-polymers00
Water18010
1
A: TAL effector
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)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)62,3113
Polymers62,3113
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-53 kcal/mol
Surface area25040 Å2
MethodPISA
2
B: TAL effector
C: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)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)62,3113
Polymers62,3113
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-52 kcal/mol
Surface area24570 Å2
MethodPISA
3
E: TAL effector
F: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)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)62,3113
Polymers62,3113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-54 kcal/mol
Surface area24690 Å2
MethodPISA
4
H: TAL effector
K: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)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)62,3113
Polymers62,3113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-54 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.169, 93.622, 167.632
Angle α, β, γ (deg.)90.00, 102.80, 90.00
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
11METMETHISHISAA230 - 7261 - 497
21METMETHISHISBD230 - 7261 - 497
12METMETHISHISAA230 - 7261 - 497
22METMETHISHISEG230 - 7261 - 497
13METMETHISHISAA230 - 7261 - 497
23METMETHISHISHJ230 - 7261 - 497
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
110METMETHISHISBD230 - 7261 - 497
210METMETHISHISEG230 - 7261 - 497
111METMETHISHISBD230 - 7261 - 497
211METMETHISHISHJ230 - 7261 - 497
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
116METMETHISHISEG230 - 7261 - 497
216METMETHISHISHJ230 - 7261 - 497
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*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')


Mass: 5110.309 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
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→50 Å / Num. obs: 73997 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rrim(I) all: 0.092 / Net I/σ(I): 2
Reflection shellResolution: 3.09→3.18 Å / Num. unique obs: 43876 / Rrim(I) all: 0.092

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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: 3.1→50 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.861 / SU B: 59.633 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.57
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27782 2348 5.1 %RANDOM
Rwork0.24264 ---
obs0.24442 73997 89.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.589 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å2-0 Å22 Å2
2---1.58 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14420 2764 0 10 17194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01817732
X-RAY DIFFRACTIONr_bond_other_d0.0050.0216368
X-RAY DIFFRACTIONr_angle_refined_deg1.341.82924756
X-RAY DIFFRACTIONr_angle_other_deg1.268337608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02251984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09825.839548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.776152376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4771568
X-RAY DIFFRACTIONr_chiral_restr0.080.22880
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118640
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023732
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_it0.630.8287948
X-RAY DIFFRACTIONr_mcbond_other0.6280.8287947
X-RAY DIFFRACTIONr_mcangle_it1.1491.2379928
X-RAY DIFFRACTIONr_mcangle_other1.1481.2389929
X-RAY DIFFRACTIONr_scbond_it0.4940.859784
X-RAY DIFFRACTIONr_scbond_other0.4940.859785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9091.26414829
X-RAY DIFFRACTIONr_long_range_B_refined2.4866.86820994
X-RAY DIFFRACTIONr_long_range_B_other2.4876.86220992
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)
11A300800.08
12B300800.08
21A302060.07
22E302060.07
31A302990.07
32H302990.07
41I14050.08
42C14050.08
51I13960.08
52F13960.08
61I13970.09
62K13970.09
71J12600.07
72D12600.07
81J12600.08
82G12600.08
91J12580.07
92L12580.07
101B305220.06
102E305220.06
111B306180.06
112H306180.06
121C13980.08
122F13980.08
131C14000.08
132K14000.08
141D12780.02
142G12780.02
151D12640.03
152L12640.03
161E310250.03
162H310250.03
171F14220.06
172K14220.06
181G12770.05
182L12770.05
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 73 -
Rwork0.337 1399 -
obs--38.64 %
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)
11.54560.6215-0.75913.0582-1.29812.44680.0446-0.0139-0.08940.5808-0.1373-0.1069-0.44890.44140.09270.3993-0.0733-0.15310.4751-0.00340.353126.15710.457960.1539
23.88531.2402-2.72783.12480.87913.05490.42330.1528-0.01290.5956-0.2507-0.184-0.145-0.2518-0.17260.5451-0.1002-0.08720.35340.10610.279424.0808-3.330165.7184
33.82390.4073-0.07473.5835-2.78356.4619-0.0427-0.22660.11051.07930.04610.4529-1.09940.1225-0.00330.62060.02050.00550.28530.00160.365322.0709-2.621266.8153
41.67310.37260.30943.32340.69523.7667-0.18520.01130.1072-0.14380.2030.0088-0.0114-0.164-0.01780.0516-0.0019-0.10130.49590.04350.309146.2124-46.051723.2439
51.8528-0.373-1.41133.068-2.72864.1513-0.0479-0.3441-0.0422-0.13960.05040.10560.17680.4726-0.00250.1152-0.1427-0.07850.5598-0.09030.275948.0636-49.90817.566
63.99960.1162.30633.67151.67885.87230.1410.04950.1064-0.7939-0.0107-0.5793-0.6818-0.1615-0.13030.3686-0.18370.01650.40630.04360.294949.8531-49.147516.305
73.2111-1.6655-1.46462.73620.73673.06410.38480.2637-0.085-0.6412-0.5938-0.1410.07380.01470.20890.52070.0946-0.09330.496-0.04530.504676.7334-53.399960.7011
80.8393-1.8735-0.86916.4541-0.82884.34890.2401-0.0127-0.0749-0.8386-0.27940.08220.09190.31490.03930.43290.10090.05340.4828-0.14330.508682.8744-56.523658.3384
97.9675-0.991-0.16234.25871.38444.3067-0.49870.3892-0.4588-0.64220.1344-0.20830.07770.07360.36430.61580.19260.05010.38560.11680.517182.7114-58.834957.7695
103.34890.70050.10862.0516-0.34773.720.07550.18040.03260.1766-0.25390.04890.40750.07690.17840.33070.0851-0.07750.4064-0.02260.3893.7026-6.02119.5681
111.07191.4067-2.15656.93770.05556.2488-0.06430.2672-0.04110.2907-0.03890.26350.6328-0.57620.10320.19850.0529-0.14490.4278-0.00660.315387.3433-9.263221.1203
127.5474-0.04242.59174.4061-0.14764.2634-0.4308-0.2776-0.42380.49670.16060.2820.7576-0.19950.27020.3967-0.08780.04290.479-0.04960.538587.4715-11.465321.6754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A230 - 726
2X-RAY DIFFRACTION2I-2 - 14
3X-RAY DIFFRACTION3J-14 - 2
4X-RAY DIFFRACTION4B230 - 726
5X-RAY DIFFRACTION5C-2 - 14
6X-RAY DIFFRACTION6D-14 - 2
7X-RAY DIFFRACTION7E230 - 726
8X-RAY DIFFRACTION8F-2 - 14
9X-RAY DIFFRACTION9G-14 - 2
10X-RAY DIFFRACTION10H230 - 726
11X-RAY DIFFRACTION11K-2 - 14
12X-RAY DIFFRACTION12L-14 - 2

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