[English] 日本語
Yorodumi
- PDB-7l6s: Crystal structure of the ATPase and transducer domains of DNA top... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l6s
TitleCrystal structure of the ATPase and transducer domains of DNA topoisomerase II from Balamuthia mandrillaris CDC:V039: baboon/San Diego/1986
ComponentsDNA topoisomerase II
KeywordsISOMERASE / SSGCID / DNA topoisomerase II / Balamuthia mandrillaris / ATPase domain / transducer domains / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function and homology information
Biological speciesBalamuthia mandrillaris (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of the ATPase and transducer domains of DNA topoisomerase II from Balamuthia mandrillaris Lepto ID: CDC:V039: baboon/San Diego/1986
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9976
Polymers48,2801
Non-polymers7175
Water5,314295
1
A: DNA topoisomerase II
hetero molecules

A: DNA topoisomerase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,99412
Polymers96,5602
Non-polymers1,43310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7520 Å2
ΔGint-22 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.770, 187.250, 61.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein DNA topoisomerase II


Mass: 48280.090 Da / Num. of mol.: 1 / Fragment: ATPase and transducer domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Balamuthia mandrillaris (eukaryote) / Strain: CDC:V039: baboon/San Diego/1986 / Plasmid: BamaA.19955.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18 mg/mL BamaA.19955.b.B2.PW38788 in Microlytics MCSG1 screen, condition a1 (20% w/v PEG2000, 100 mM HEPES free acid / NaOH, pH 7.5) + 3 mM magnesium chloride/AMPPNP, tray 315297 a1, ...Details: 18 mg/mL BamaA.19955.b.B2.PW38788 in Microlytics MCSG1 screen, condition a1 (20% w/v PEG2000, 100 mM HEPES free acid / NaOH, pH 7.5) + 3 mM magnesium chloride/AMPPNP, tray 315297 a1, cryoprotectant: 20% ethylene glycol + magnesium chloride/AMPPNP, puck cgp8-1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 2020 / Details: BERYIILUM LENSES
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 37513 / % possible obs: 100 % / Redundancy: 6.719 % / Biso Wilson estimate: 39.655 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Χ2: 0.937 / Net I/σ(I): 21.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-26.810.5953.327430.9140.645100
2-2.066.8210.4584.3526590.9550.496100
2.06-2.126.820.365.5826060.9570.39100
2.12-2.186.8160.2747.1925120.9770.297100
2.18-2.256.8090.2119.1624520.9850.229100
2.25-2.336.8230.16911.2223730.990.183100
2.33-2.426.820.14213.3522870.9920.154100
2.42-2.526.7870.10916.9722120.9950.118100
2.52-2.636.7940.09419.1621130.9960.101100
2.63-2.766.7680.07423.4620320.9980.08100
2.76-2.916.7540.06426.7919450.9980.069100
2.91-3.086.7170.05231.8218500.9980.056100
3.08-3.36.6330.04635.6917080.9990.05100
3.3-3.566.6050.03940.9216300.9990.043100
3.56-3.96.5790.03544.1914860.9990.038100
3.9-4.366.5440.03246.2513630.9990.035100
4.36-5.036.5080.0348.0912120.9990.032100
5.03-6.176.4910.0347.7810400.9990.032100
6.17-8.726.2630.02947.538130.9990.03199.9
8.72-505.5370.02847.134770.9990.03197.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4 4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZXM (as per MoRDa)

1zxm


Resolution: 1.95→39.74 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.3408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 2066 5.51 %0
Rwork0.1671 35437 --
obs0.1686 37503 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 44 295 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713269
X-RAY DIFFRACTIONf_angle_d0.80014455
X-RAY DIFFRACTIONf_chiral_restr0.0552502
X-RAY DIFFRACTIONf_plane_restr0.0067594
X-RAY DIFFRACTIONf_dihedral_angle_d12.95641229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.30511380.26862325X-RAY DIFFRACTION100
2-2.050.2751370.22682323X-RAY DIFFRACTION100
2.05-2.10.22661310.20772323X-RAY DIFFRACTION99.96
2.1-2.160.22411510.19162319X-RAY DIFFRACTION99.96
2.16-2.230.18341320.17692359X-RAY DIFFRACTION100
2.23-2.310.20461630.1732307X-RAY DIFFRACTION100
2.31-2.40.20081520.18082339X-RAY DIFFRACTION100
2.4-2.510.21871450.17442330X-RAY DIFFRACTION100
2.51-2.650.20071130.17492361X-RAY DIFFRACTION100
2.65-2.810.20081460.16752357X-RAY DIFFRACTION99.96
2.81-3.030.18551430.17122361X-RAY DIFFRACTION100
3.03-3.330.23741260.17422381X-RAY DIFFRACTION100
3.33-3.820.18971300.15652394X-RAY DIFFRACTION100
3.82-4.810.15741260.13612431X-RAY DIFFRACTION99.96
4.81-39.740.17561330.1642527X-RAY DIFFRACTION99.59
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)
12.460364148120.458108685670.4792893947741.58595508404-0.2969611189172.75415415723-0.1655453105620.2296340848520.0777496377304-0.09968638281080.0764076014577-0.190925399438-0.5441326021980.3968918709750.03794652644710.222558502806-0.02776224164050.01949746352780.2173311292060.03495710634120.21818515461911.445318187928.3892826945-16.7742590223
22.57250057053-0.1481708616660.8479703396932.208580431320.1072537364931.84583060484-0.0466480605985-0.0284957014541-0.2911662206430.1904108539590.0108100667597-0.384658489661-0.02925746663840.2870333859270.0335464379070.168569281857-0.00759569065142-0.02908500835470.2491717523540.05233148137130.287959483417.830044878519.7623657893-4.2358065893
32.40505493736-0.664852040644-0.9598876307224.68816099757-0.3143802291340.8297784360820.123741021928-0.2123612652460.4514448497750.417184280089-0.0294851421146-0.179923246476-0.2521546838530.0190530606039-0.0841394679440.319907912240.00274133662088-0.03097313453260.287482124061-0.03822871205280.192194189712.0919245028749.9220825917-1.53309901145
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 119 through 191 )119 - 1911 - 73
22chain 'A' and (resid 192 through 365 )192 - 36574 - 247
33chain 'A' and (resid 366 through 519 )366 - 519248 - 396

+
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://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