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- PDB-6zt3: N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyr... -

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Basic information

Entry
Database: PDB / ID: 6zt3
TitleN-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ATPASE DOMAIN / GHKL SUPERFAMILY
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsFeng, L. / Mundy, J.E.A. / Stevenson, C.E.M. / Mitchenall, L.A. / Lawson, D.M. / Mi, K. / Maxwell, A.
Funding support United Kingdom, China, 7items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)CEPAMS United Kingdom
Wellcome Trust110072/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
Ministry of Science and Technology (MoST, China)2018YFC1603900 China
Ministry of Science and Technology (MoST, China)2017YFA0505901 China
National Natural Science Foundation of China (NSFC)31970136 China
National Natural Science Foundation of China (NSFC)31670137 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic.
Authors: Feng, L. / Mundy, J.E.A. / Stevenson, C.E.M. / Mitchenall, L.A. / Lawson, D.M. / Mi, K. / Maxwell, A.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,96612
Polymers47,0181
Non-polymers94911
Water5,332296
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,93324
Polymers94,0352
Non-polymers1,89822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area11180 Å2
ΔGint-58 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.985, 76.985, 261.476
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-510-

NA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA gyrase subunit B


Mass: 47017.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-427 of the wild-type sequence with a serine residue appended to the N-terminus left after cleavage of the affinity tag
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: gyrB, MSMEG_0005, MSMEI_0007 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QNE0, EC: 5.99.1.3

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Non-polymers , 6 types, 307 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / 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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→65.37 Å / Num. obs: 66509 / % possible obs: 100 % / Redundancy: 38.8 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.023 / Rrim(I) all: 0.143 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.5939.52.48612767432310.8450.3992.5181.9100
8.54-65.3727.90.0341504954010.0060.03562.399.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASER2.82phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKB

3zkb


Resolution: 1.56→64.69 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 5.159 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0777 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 3287 5 %RANDOM
Rwork0.1469 ---
obs0.1493 63082 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.92 Å2 / Biso mean: 23.46 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.92 Å2-0 Å2
2---1.84 Å20 Å2
3---5.98 Å2
Refinement stepCycle: final / Resolution: 1.56→64.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 57 302 3392
Biso mean--24.98 36.44 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133264
X-RAY DIFFRACTIONr_bond_other_d0.0070.0172955
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.6514436
X-RAY DIFFRACTIONr_angle_other_deg1.441.586855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8422.629175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12515536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3781521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02687
X-RAY DIFFRACTIONr_rigid_bond_restr3.04336218
LS refinement shellResolution: 1.56→1.601 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 247 -
Rwork0.251 4566 -
all-4813 -
obs--99.98 %

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