[English] 日本語
Yorodumi
- PDB-6bq9: 2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bq9
Title2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-493) of DNA Topoisomerase IV Subunit A from Pseudomonas putida
ComponentsDNA topoisomerase 4 subunit A
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DNA Topoisomerase IV
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase IV, subunit A, Gram-negative / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...DNA topoisomerase IV, subunit A, Gram-negative / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / Gyrase A; domain 2 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 4 subunit A
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-493) of DNA Topoisomerase IV Subunit A from Pseudomonas putida.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 4 subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1603
Polymers56,1021
Non-polymers582
Water1,36976
1
A: DNA topoisomerase 4 subunit A
hetero molecules

A: DNA topoisomerase 4 subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3216
Polymers112,2042
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3770 Å2
ΔGint-58 kcal/mol
Surface area42490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.494, 224.057, 115.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DNA topoisomerase 4 subunit A / Topoisomerase IV subunit A


Mass: 56102.012 Da / Num. of mol.: 1 / Fragment: N-terminal Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: parC, PP_4912 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q88DB5, EC: 5.99.1.3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 4.16 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C1), 3.5M Sodium formate pH (7.0); Cryo: 4.0M Sodium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 30230 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Χ2: 1.008 / Net I/σ(I): 28.3
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1450 / CC1/2: 0.903 / Rpim(I) all: 0.316 / Rrim(I) all: 0.848 / Rsym value: 0.785 / Χ2: 1.007 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EIX

5eix


Resolution: 2.55→29.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 29.725 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24654 1487 4.9 %RANDOM
Rwork0.20765 ---
obs0.20958 28738 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 95.211 Å2
Baniso -1Baniso -2Baniso -3
1-10.4 Å20 Å20 Å2
2---8.77 Å20 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.55→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3627 0 2 76 3705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193688
X-RAY DIFFRACTIONr_bond_other_d0.0010.023550
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9824993
X-RAY DIFFRACTIONr_angle_other_deg0.8938207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0715456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.99223.446177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.37915672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4861540
X-RAY DIFFRACTIONr_chiral_restr0.080.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0214081
X-RAY DIFFRACTIONr_gen_planes_other0.020.02727
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_it3.0217.0231827
X-RAY DIFFRACTIONr_mcbond_other3.0037.021826
X-RAY DIFFRACTIONr_mcangle_it4.81410.5312282
X-RAY DIFFRACTIONr_mcangle_other4.81410.5342283
X-RAY DIFFRACTIONr_scbond_it3.0917.2961861
X-RAY DIFFRACTIONr_scbond_other3.097.2991862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.96510.822712
X-RAY DIFFRACTIONr_long_range_B_refined7.32982.9934092
X-RAY DIFFRACTIONr_long_range_B_other7.32682.9714089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 88 -
Rwork0.419 1951 -
obs--91.6 %
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)
13.02351.33082.22940.59831.19755.94410.0785-0.00830.01990.04220.01220.01940.43170.2536-0.09070.10570.0546-0.09160.0471-0.02720.1665-4.7599-33.174516.6466
23.6584-0.83330.84082.01080.01126.44170.17220.1146-0.0869-0.16280.03240.13640.25950.6199-0.20450.10570.0118-0.07860.0794-0.03850.111-2.2927-30.977714.7055
32.6338-0.22140.50240.3564-0.31693.4769-0.12580.2098-0.0175-0.15550.05550.1171-0.24070.01490.07030.18070.0074-0.06650.1078-0.01510.1948-12.6841-33.55166.7232
44.0722-2.78760.03163.09840.40730.3617-0.00090.4326-0.1537-0.5243-0.18210.2067-0.20040.04940.1830.2498-0.0026-0.06190.2299-0.03710.1261-7.4551-46.9674-7.7829
55.9604-4.8858-1.53684.82121.50313.63370.09370.365-0.2011-0.419-0.31270.102-0.2359-0.02090.21910.1615-0.03080.00570.1673-0.01470.10531.6781-56.3165-10.0271
60.87321.43520.63225.29992.53421.886-0.0005-0.0780.1204-0.0659-0.22510.7725-0.5104-0.31630.22560.62360.1552-0.06570.12240.00720.2545-14.9547-2.292615.6603
71.8975-0.849-0.497710.24332.50791.35870.08990.27290.2012-0.9932-0.2798-0.0268-0.4119-0.01160.18990.28570.0359-0.09530.06390.050.1079-11.7854-25.5727-6.3092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 105
2X-RAY DIFFRACTION2A106 - 157
3X-RAY DIFFRACTION3A158 - 194
4X-RAY DIFFRACTION4A195 - 297
5X-RAY DIFFRACTION5A298 - 334
6X-RAY DIFFRACTION6A335 - 463
7X-RAY DIFFRACTION7A464 - 491

+
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