[English] 日本語
Yorodumi
- PDB-5lut: Structures of DHBN domain of Gallus gallus BLM helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lut
TitleStructures of DHBN domain of Gallus gallus BLM helicase
ComponentsBLM helicase
KeywordsTRANSFERASE / helicase dimerization alpha-helix motif
Function / homology
Function and homology information


regulation of DNA-templated DNA replication / forked DNA-dependent helicase activity / G-quadruplex DNA unwinding / four-way junction helicase activity / DNA double-strand break processing / DNA duplex unwinding / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / four-way junction DNA binding ...regulation of DNA-templated DNA replication / forked DNA-dependent helicase activity / G-quadruplex DNA unwinding / four-way junction helicase activity / DNA double-strand break processing / DNA duplex unwinding / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / four-way junction DNA binding / DNA helicase activity / telomere maintenance / double-strand break repair via homologous recombination / protein homooligomerization / protein complex oligomerization / chromosome / single-stranded DNA binding / DNA recombination / DNA helicase / DNA repair / protein homodimerization activity / DNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
RecQ-like DNA helicase BLM, N-terminal domain / N-terminal region of Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type ...RecQ-like DNA helicase BLM, N-terminal domain / N-terminal region of Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / Bloom syndrome protein homolog / Bloom syndrome protein homolog
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsShi, J. / Chen, W.-F. / Zhang, B. / Fan, S.-H. / Ai, X. / Liu, N.-N. / Rety, S. / Xi, X.-G.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation.
Authors: Shi, J. / Chen, W.F. / Zhang, B. / Fan, S.H. / Ai, X. / Liu, N.N. / Rety, S. / Xi, X.G.
History
DepositionSep 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLM helicase
B: BLM helicase
C: BLM helicase
D: BLM helicase
E: BLM helicase
F: BLM helicase
G: BLM helicase
H: BLM helicase
I: BLM helicase
J: BLM helicase
K: BLM helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,24015
Polymers84,86011
Non-polymers3804
Water73941
1
K: BLM helicase

J: BLM helicase


Theoretical massNumber of molelcules
Total (without water)15,4292
Polymers15,4292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
2
A: BLM helicase
B: BLM helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5243
Polymers15,4292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-39 kcal/mol
Surface area6810 Å2
MethodPISA
3
C: BLM helicase
D: BLM helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5243
Polymers15,4292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-38 kcal/mol
Surface area6950 Å2
MethodPISA
4
E: BLM helicase

E: BLM helicase


Theoretical massNumber of molelcules
Total (without water)15,4292
Polymers15,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2820 Å2
ΔGint-35 kcal/mol
Surface area6600 Å2
MethodPISA
5
F: BLM helicase
G: BLM helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5243
Polymers15,4292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-38 kcal/mol
Surface area6890 Å2
MethodPISA
6
H: BLM helicase
I: BLM helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5243
Polymers15,4292
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-37 kcal/mol
Surface area6100 Å2
MethodPISA
7
J: BLM helicase

K: BLM helicase


Theoretical massNumber of molelcules
Total (without water)15,4292
Polymers15,4292
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area430 Å2
ΔGint-6 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.686, 230.804, 50.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
BLM helicase


Mass: 7714.577 Da / Num. of mol.: 11 / Fragment: UNP residues 97-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: RCJMB04_17c23 / Plasmid: pET15b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZJM1, UniProt: Q9I920*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M MgCl2 0.1M Na-Citrate 12% PEG 1500 15% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.718→54.302 Å / Num. obs: 25224 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 75.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1144 / Net I/σ(I): 18.48
Reflection shellHighest resolution: 2.815 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.8552 / Mean I/σ(I) obs: 2.23 / CC1/2: 0.802 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→72.774 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 1234 4.96 %5%
Rwork0.2364 ---
obs0.2387 24904 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→72.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 20 41 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094093
X-RAY DIFFRACTIONf_angle_d1.1195516
X-RAY DIFFRACTIONf_dihedral_angle_d3.2832588
X-RAY DIFFRACTIONf_chiral_restr0.051682
X-RAY DIFFRACTIONf_plane_restr0.006699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7201-2.8290.38471490.36892421X-RAY DIFFRACTION93
2.829-2.95770.3921310.33632533X-RAY DIFFRACTION97
2.9577-3.11370.3741300.29332585X-RAY DIFFRACTION100
3.1137-3.30880.32011220.28282642X-RAY DIFFRACTION100
3.3088-3.56420.34011400.2722622X-RAY DIFFRACTION100
3.5642-3.92290.28021510.22942642X-RAY DIFFRACTION100
3.9229-4.49050.2441400.18462649X-RAY DIFFRACTION100
4.4905-5.65720.25981310.22442731X-RAY DIFFRACTION100
5.6572-72.80020.24451400.21782845X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.933-0.64660.18694.5169-0.43284.3044-0.06930.08880.388-0.34450.29370.14420.18770.2893-0.14470.37890.0261-0.00970.38590.01950.4877-38.925847.592642.6193
26.69933.1205-2.39464.2913-0.63444.11710.3617-0.64030.23860.5955-0.269-0.6987-0.27970.6494-0.01780.33240.0922-0.06040.506-0.01820.4818-28.706951.380948.479
34.44271.189-1.61822.2125-0.68842.31850.27710.91520.27440.00640.1283-0.7417-0.21190.2655-0.1930.45420.1090.07660.61470.01160.6449-28.631244.123841.3814
41.6176-0.5057-0.63942.81060.69943.3364-0.1410.1109-0.0198-0.1380.11840.31320.2116-0.5145-0.10580.51410.0134-0.1040.41790.10420.4771-45.67641.221742.1181
55.0859-2.5781-0.23824.26990.30142.4973-0.1914-0.3767-0.3835-0.50540.4166-0.78530.11470.5909-0.16150.6024-0.08910.12050.6307-0.01380.6229-32.944123.820535.4226
65.52963.0074-1.49398.4797-0.88334.276-0.3743-0.1380.4183-0.51940.27561.5367-0.5294-1.4860.280.53870.1474-0.12370.66930.03310.5492-54.863427.022837.4151
74.8281.58141.21444.63010.81733.5923-0.0539-0.10240.08380.57320.0248-0.2031-0.1035-0.2651-0.02830.54520.09080.00730.52050.05180.4556-41.703429.33547.4471
84.1363-0.64361.26264.07280.15343.9691-0.2324-0.3514-0.53220.4770.0087-0.5990.05040.82980.17160.55210.05340.00340.62240.08720.4686-35.238721.747245.9141
91.8972-2.81861.36686.75990.90274.34670.6070.5165-0.2473-0.3877-0.80190.6560.3337-1.0751-0.05080.5793-0.0319-0.0930.57490.00440.5219-53.151221.697730.6097
104.112-0.95450.25973.66920.28552.5898-0.0730.6052-0.0366-0.80830.003-0.59880.40960.01180.10390.6545-0.07710.14170.4406-0.01480.5247-37.394916.720129.6897
113.9074-0.96371.4154.7272-0.7614.62570.104-0.80480.35520.5746-0.0123-0.7386-0.5885-0.2145-0.1510.508-0.0461-0.04340.5416-0.09530.6734-33.39591.003341.1258
124.604-0.25870.22825.20940.39593.94740.39850.9099-0.0066-0.7136-0.08440.5231-0.2361-0.114-0.0640.51130.0068-0.03250.52250.11350.5214-45.25385.61831.082
134.40120.33510.25223.8037-1.34755.61890.0020.84260.1271-1.244-0.0181-0.31710.46870.3519-0.22330.6565-0.01220.00420.54940.00350.5115-29.500666.95233.5703
143.13141.54951.2123.91860.33333.95760.2403-0.6228-0.21090.5266-0.30720.34120.1166-0.2996-0.01160.35270.06730.09320.50790.06250.5014-34.920363.800150.9102
154.02932.06631.71634.19870.79624.7644-0.520.32180.6027-0.46010.17051.2735-0.1788-0.25680.28010.3860.1044-0.05410.43340.01480.6238-38.006869.864240.6239
163.1691-1.2871-0.6123.1322-0.56143.87520.13530.0384-0.0582-0.2690.0594-0.0476-0.17160.384-0.07980.4419-0.06420.07330.416-0.11910.3882-21.837972.736942.7162
174.5176-1.2071.0323.94290.27092.9090.69430.60620.4279-0.28520.07691.6356-0.6346-1.8909-0.60070.56810.1262-0.00581.0640.17040.9525-34.110188.056433.6481
184.45333.17360.55745.1129-2.42566.1304-0.0784-0.6811-0.38471.2418-0.2053-0.8385-0.58851.24220.18050.65740.09210.08220.6691-0.05780.5746-13.778789.004838.9668
195.7043-0.289-1.18493.8275-1.27137.2850.8015-0.6661-0.08760.3507-0.3330.7839-1.66160.3916-0.19090.6350.05860.10070.3753-0.07030.4837-28.261984.538346.9606
203.35780.3708-1.16231.9124-0.38673.66510.26240.15140.84011.21160.4930.8751-0.9635-1.4262-0.80970.87240.16310.33680.66520.05420.8463-33.15592.266443.1503
211.9335-2.25680.45546.85951.04362.84730.3142-0.81850.54170.899-0.08890.2393-0.66790.8345-0.31110.7163-0.04490.10110.5934-0.09220.5578-15.249693.237130.6995
224.06570.57953.00164.8393.14183.82810.79862.00330.2765-1.17471.62290.2569-0.2225-1.3136-0.31590.64440.07210.07830.78670.62780.5854-28.391894.146727.3963
233.37532.6857-1.22792.51-1.24270.6236-0.32130.61170.1379-1.42510.6477-0.08910.8616-1.6404-0.01581.61760.1236-0.11371.34360.36461.0701-37.2792108.20230.2537
242.08-0.84390.15131.34511.72834.6186-1.04190.98991.2229-1.362-0.9654-0.26540.0291-0.23711.03671.53740.3380.07031.96120.06511.0978-28.4163105.813418.3812
251.3294-0.6735-0.61272.5139-1.6962.1481-0.3997-1.743-0.7737-0.1104-0.38610.1395-0.354-0.46840.55042.00320.1213-0.18674.0340.30780.863-24.6361112.214525.4802
260.21190.2042-0.2740.2665-0.21850.38130.1438-0.0893-0.433-0.2909-0.0794-0.2107-0.0548-0.10620.04423.46341.0028-0.51270.9284-1.62960.732-25.9258103.696439.7536
277.442-0.4655-0.06267.4422-1.12580.1696-0.9028-0.495-1.3725-0.77430.5222-0.2938-0.5518-0.98010.221.92540.030.03271.7161-0.00840.8746-47.8233117.588242.6632
283.6164-0.56950.59634.8857-2.23251.2543-0.0531-0.53091.38260.1422-0.1250.0856-0.14040.45790.13410.4985-0.2265-0.34591.37190.21231.3516-43.0287112.685426.2705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 310 through 341 )
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 361 )
3X-RAY DIFFRACTION3chain 'B' and (resid 309 through 330 )
4X-RAY DIFFRACTION4chain 'B' and (resid 331 through 361 )
5X-RAY DIFFRACTION5chain 'C' and (resid 310 through 330 )
6X-RAY DIFFRACTION6chain 'C' and (resid 331 through 341 )
7X-RAY DIFFRACTION7chain 'C' and (resid 342 through 361 )
8X-RAY DIFFRACTION8chain 'D' and (resid 308 through 330 )
9X-RAY DIFFRACTION9chain 'D' and (resid 331 through 341 )
10X-RAY DIFFRACTION10chain 'D' and (resid 342 through 361 )
11X-RAY DIFFRACTION11chain 'E' and (resid 310 through 330 )
12X-RAY DIFFRACTION12chain 'E' and (resid 331 through 361 )
13X-RAY DIFFRACTION13chain 'F' and (resid 307 through 330 )
14X-RAY DIFFRACTION14chain 'F' and (resid 331 through 361 )
15X-RAY DIFFRACTION15chain 'G' and (resid 310 through 330 )
16X-RAY DIFFRACTION16chain 'G' and (resid 331 through 361 )
17X-RAY DIFFRACTION17chain 'H' and (resid 312 through 330 )
18X-RAY DIFFRACTION18chain 'H' and (resid 331 through 343 )
19X-RAY DIFFRACTION19chain 'H' and (resid 344 through 361 )
20X-RAY DIFFRACTION20chain 'I' and (resid 310 through 330 )
21X-RAY DIFFRACTION21chain 'I' and (resid 331 through 341 )
22X-RAY DIFFRACTION22chain 'I' and (resid 342 through 357 )
23X-RAY DIFFRACTION23chain 'J' and (resid 320 through 328 )
24X-RAY DIFFRACTION24chain 'J' and (resid 329 through 338 )
25X-RAY DIFFRACTION25chain 'J' and (resid 339 through 351 )
26X-RAY DIFFRACTION26chain 'J' and (resid 352 through 359 )
27X-RAY DIFFRACTION27chain 'K' and (resid 311 through 320 )
28X-RAY DIFFRACTION28chain 'K' and (resid 321 through 332 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more