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- PDB-4kpy: DNA binding protein and DNA complex structure -

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Basic information

Entry
Database: PDB / ID: 4kpy
TitleDNA binding protein and DNA complex structure
Components
  • DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
  • DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
  • Uncharacterized protein
KeywordsDNA BINDING PROTEIN/DNA / Argonaute / RNA interference / DNA interference / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / manganese ion binding / DNA replication / DNA binding / RNA binding
Similarity search - Function
Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 ...Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #60 / Alpha-Beta Plaits - #2620 / Argonaute, PAZ domain / Argonaute PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain profile. / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-MONOPHOSPHATE / : / DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.406 Å
AuthorsSheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Wang, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.
Authors: Sheng, G. / Zhao, H. / Wang, J. / Rao, Y. / Tian, W. / Swarts, D.C. / van der Oost, J. / Patel, D.J. / Wang, Y.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
D: DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
E: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
F: DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
M: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
N: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,93616
Polymers177,9628
Non-polymers9748
Water6,413356
1
A: Uncharacterized protein
C: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
D: DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
N: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4688
Polymers88,9814
Non-polymers4874
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-58 kcal/mol
Surface area30740 Å2
MethodPISA
2
B: Uncharacterized protein
E: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
F: DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
M: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4688
Polymers88,9814
Non-polymers4874
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-65 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.329, 118.362, 160.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 76728.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_P0026 / Plasmid: pET-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q746M7

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DNA chain , 3 types, 6 molecules CEDFMN

#2: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')


Mass: 6588.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')


Mass: 2979.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')


Mass: 2683.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 364 molecules

#5: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P / Comment: dTMP*YM
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 306 K / Method: hanging drop / pH: 7
Details: 2.6M NaAc, 0.1M Bis-Tris Propane pH 7.0, hanging drop, temperature 306K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorDetector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 82290 / Redundancy: 5.4 % / Biso Wilson estimate: 44.73 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Num. unique all: 7757 / % possible all: 92.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→48.312 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8128 / SU ML: 0.33 / σ(F): 1.33 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4028 4.99 %radom
Rwork0.1904 ---
obs0.1926 80659 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.75 Å2 / Biso mean: 49.8736 Å2 / Biso min: 15.25 Å2
Refinement stepCycle: LAST / Resolution: 2.406→48.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 1314 48 356 12260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912349
X-RAY DIFFRACTIONf_angle_d1.10217084
X-RAY DIFFRACTIONf_chiral_restr0.0451870
X-RAY DIFFRACTIONf_plane_restr0.0051984
X-RAY DIFFRACTIONf_dihedral_angle_d17.9734667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4059-2.43420.28741180.25712346246487
2.4342-2.46390.32921320.254626942826100
2.4639-2.49510.34981400.277926762816100
2.4951-2.52790.43261450.35412599274498
2.5279-2.56250.39881500.297226942844100
2.5625-2.59910.35641380.264326902828100
2.5991-2.63790.29781400.254926892829100
2.6379-2.67920.47381250.37082684280999
2.6792-2.72310.36871350.28432698283399
2.7231-2.770.30211440.218126742818100
2.77-2.82040.27591530.219926952848100
2.8204-2.87460.27411410.21326842825100
2.8746-2.93330.26661630.209326962859100
2.9333-2.99710.24681340.208226862820100
2.9971-3.06680.27221420.206126952837100
3.0668-3.14350.24551170.195427442861100
3.1435-3.22840.2281440.191727012845100
3.2284-3.32340.21221420.18227222864100
3.3234-3.43070.20811420.17952667280999
3.4307-3.55320.24551470.21672653280098
3.5532-3.69550.22691080.18231824193267
3.6955-3.86360.22141190.17112699281899
3.8636-4.06720.23211100.16072010212074
4.0672-4.32180.16851530.143227252878100
4.3218-4.65530.1681380.136927662904100
4.6553-5.12330.20871570.144327322889100
5.1233-5.86360.20351460.174427822928100
5.8636-7.38320.24731480.184128112959100
7.3832-48.32170.17031570.16682895305299
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)
12.07510.1296-0.27850.78570.00161.08950.31240.99610.091-0.4721-0.3377-0.321-0.4346-0.17660.04860.57870.2204-0.00240.71150.06290.480411.1183-28.565844.5488
20.3795-0.0098-0.77731.20661.12882.5963-0.15360.2558-0.20570.3425-0.1060.02870.7922-0.40220.23340.60030.06120.07150.4682-0.10560.4545-13.8947-42.314938.1322
31.0607-0.10130.54690.5283-0.05011.6248-0.0933-0.07930.08280.0655-0.00190.0074-0.03750.01560.1020.19380.0116-0.00850.1815-0.03810.2165-27.7132-9.569740.1209
40.9303-0.5971-0.05432.1426-0.5111.0901-0.0795-0.16090.0940.3635-0.1418-0.3195-0.24310.1690.19560.34280.0538-0.02940.48780.0390.34314.7483-25.7327-1.1616
50.4219-0.08680.01640.86380.30481.23740.00240.05360.1228-0.1115-0.0605-0.0668-0.00190.10230.06070.22420.0152-0.02460.21830.04590.2576-21.4773-2.42290.6628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:122 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 123:300 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 301:685 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 3:282 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 283:685 )

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