[English] 日本語
Yorodumi
- PDB-5cty: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cty
TitleCrystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment
ComponentsDNA gyrase subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / DNA gyrase / GyrB / fragment-based screening / structure-based design / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. ...DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-55H / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsAndersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. / Mesleh, M. / Cross, J.B. / Zhang, J. ...Andersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. / Mesleh, M. / Cross, J.B. / Zhang, J. / Yang, Q. / Lippa, B. / Ryan, M.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.
Authors: Mesleh, M.F. / Cross, J.B. / Zhang, J. / Kahmann, J. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Felicetti, B. / Wood, M. / Hadfield, A.T. / Scheich, C. / Moy, T.I. / Yang, Q. / Shotwell, ...Authors: Mesleh, M.F. / Cross, J.B. / Zhang, J. / Kahmann, J. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Felicetti, B. / Wood, M. / Hadfield, A.T. / Scheich, C. / Moy, T.I. / Yang, Q. / Shotwell, J. / Nguyen, K. / Lippa, B. / Dolle, R. / Ryan, M.D.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86912
Polymers47,8632
Non-polymers1,00610
Water6,575365
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2285
Polymers23,9321
Non-polymers2964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6417
Polymers23,9321
Non-polymers7106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.551, 55.463, 51.131
Angle α, β, γ (deg.)90.000, 100.480, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B


Mass: 23931.602 Da / Num. of mol.: 2
Fragment: ATP binding domain, UNP residues 2-234 (delta 105-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P0A0K8, EC: 5.99.1.3

-
Non-polymers , 5 types, 375 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-55H / 3-[2-(pyridin-3-yl)-1,3-thiazol-5-yl]-2,7-dihydro-6H-pyrazolo[3,4-b]pyridin-6-one


Mass: 295.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9N5OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→26.57 Å / Num. obs: 50457 / % possible obs: 97.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.047 / Χ2: 0.96 / Net I/σ(I): 11.2 / Num. measured all: 137119 / Scaling rejects: 1029
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.661.90.3442792041721.281181.1
1.66-1.722.30.2792.61152950031.141497.2
1.72-1.82.40.1943.71216950671.08698.2
1.8-1.92.510.1464.91276850901.01998.5
1.9-2.022.760.1146.31431851470.9512199.6
2.02-2.172.960.089.51529151500.865399.7
2.17-2.392.930.06911.31538551740.9722099.7
2.39-2.742.970.05714.11563951870.923699.7
2.74-3.4530.04418.61589252010.8926899.7
3.45-27.383.060.02928.11620852660.889199

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.88 Å26.57 Å
Translation1.88 Å26.57 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREKdata reduction
d*TREK9.7 W8RSSIdata scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.6→26.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2077 / WRfactor Rwork: 0.175 / FOM work R set: 0.8429 / SU B: 1.945 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0926 / SU Rfree: 0.0908 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2560 5.1 %RANDOM
Rwork0.171 ---
obs0.1725 47892 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.59 Å2 / Biso mean: 23.167 Å2 / Biso min: 8.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.34 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.6→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 65 365 3476
Biso mean--37.18 34.14 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193328
X-RAY DIFFRACTIONr_bond_other_d0.0020.023203
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9674539
X-RAY DIFFRACTIONr_angle_other_deg1.07937360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25424.674184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3711529
X-RAY DIFFRACTIONr_chiral_restr0.1210.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
X-RAY DIFFRACTIONr_mcbond_it2.0831.9451561
X-RAY DIFFRACTIONr_mcbond_other2.0671.9431560
X-RAY DIFFRACTIONr_mcangle_it3.0022.91952
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 163 -
Rwork0.428 2787 -
all-2950 -
obs--77.88 %

+
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