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- PDB-6zt5: Complex between a homodimer of Mycobacterium smegmatis MfpA and a... -

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Basic information

Entry
Database: PDB / ID: 6zt5
TitleComplex between a homodimer of Mycobacterium smegmatis MfpA and a single copy of the N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit
Components
  • DNA gyrase subunit B
  • Pentapeptide repeat protein MfpA
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ATPASE DOMAIN / GHKL SUPERFAMILY / PENTAPEPTIDE REPEAT PROTEIN / FLUOROQUINOLONE RESISTANCE / DNA GYRASE / DNA MIMICRY / RIGHT-HANDED QUADRILATERAL BETA-HELIX
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
Pentapeptide repeats (8 copies) / Pentapeptide repeats (9 copies) / Pentapeptide repeat / 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 ...Pentapeptide repeats (8 copies) / Pentapeptide repeats (9 copies) / Pentapeptide repeat / 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
DNA gyrase subunit B / Pentapeptide repeat protein MfpA
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentapeptide repeat protein MfpA
B: Pentapeptide repeat protein MfpA
C: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0046
Polymers89,7153
Non-polymers2883
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-58 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.545, 59.380, 141.217
Angle α, β, γ (deg.)90.000, 119.710, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 9 - 188 / Label seq-ID: 10 - 189

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Pentapeptide repeat protein MfpA / Mycobacterial fluoroquinone resistance pentapeptide / Orf3


Mass: 21348.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Full 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: mfpA, MSMEG_1641, MSMEI_1602 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QSY0
#2: 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, DNA topoisomerase (ATP-hydrolysing)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→75.32 Å / Num. obs: 55380 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 68.8 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 14.4
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
2.2-2.266.51.8572930644810.6080.7872.0220.8100
9.33-75.26.70.03153047950.9910.0140.03566.999.6

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZT3, 6ZT4

6zt3

6zt4


Resolution: 2.2→75.32 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 17.19 / SU ML: 0.189 / SU R Cruickshank DPI: 0.2021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2825 5.1 %RANDOM
Rwork0.208 ---
obs0.2102 52549 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.08 Å2 / Biso mean: 70 Å2 / Biso min: 42.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-1.17 Å2
2--5.46 Å20 Å2
3----3.75 Å2
Refinement stepCycle: final / Resolution: 2.2→75.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 15 86 5590
Biso mean--92.11 67.32 -
Num. residues----709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175152
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6437674
X-RAY DIFFRACTIONr_angle_other_deg1.2451.58311838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29920.381341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06815918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6421562
X-RAY DIFFRACTIONr_chiral_restr0.0570.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021339
Refine LS restraints NCS

Ens-ID: 1 / Number: 5361 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 181 -
Rwork0.371 3854 -
all-4035 -
obs--99.8 %
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)
14.20390.2029-1.29415.0361-1.83498.0102-0.0746-0.37580.25760.92150.21480.2986-0.0116-0.4264-0.14020.30090.0871-0.03660.14890.01430.1965-18.318824.270473.5552
23.7881-1.3057-2.88255.24062.30857.0461-0.43770.1672-0.21990.29890.25110.0150.5823-0.55760.18660.1322-0.0611-0.09390.09760.03060.2244-13.472317.924660.5456
33.8315-2.1352-1.92547.98720.27035.7917-0.27710.3384-0.0334-0.07540.0237-0.13130.4269-0.48220.25340.0902-0.0676-0.06860.06680.01420.1762-10.66916.111851.2767
43.93580.1862-2.9532.35641.2498.2784-0.11840.5335-0.0957-0.44390.023-0.08310.3731-0.24170.09540.2446-0.071-0.04750.1644-0.04460.2505-7.833412.812841.7746
54.518-5.50775.97998.955-5.050310.18630.42780.63070.2541-0.6759-0.694-0.44570.52290.94150.26620.5930.11480.04290.6193-0.00730.335411.3065-14.6762-2.5321
66.51762.42811.16244.07271.01114.33940.10670.157-0.4419-0.429-0.196-0.38030.0410.57320.08930.3980.0875-0.08550.4695-0.03990.136714.6866-9.80612.2246
71.6147-0.0988-0.52223.26080.58934.28270.0994-0.04780.07340.0061-0.10330.1250.08750.27580.00390.2634-0.014-0.12660.31790.00390.1128.0032-2.806614.5032
83.7176-1.293-2.95183.38120.99846.89580.1204-0.17030.1627-0.075-0.12660.14020.03350.07520.00620.3-0.0906-0.09310.2272-0.03090.1807-1.35125.232529.4884
92.85130.8123-0.47236.73110.6123.0906-0.07850.69990.0521-0.4295-0.049-0.8949-0.03150.41850.12750.1938-0.0727-0.09860.7876-0.0040.3948-37.526930.991121.1856
103.34050.26091.45142.37470.82185.9666-0.02730.652-0.1313-0.30160.0072-0.46710.37540.55650.02020.1905-0.0429-0.0540.5905-0.01710.2915-41.151827.496821.8725
115.13594.20650.85447.66210.05632.455-0.0275-0.0009-0.10220.0103-0.10520.03740.2769-0.05960.13270.1671-0.00550.00330.29290.00370.2277-46.361627.926338.8604
126.4290.26231.22483.00660.27495.7659-0.15730.99510.2214-0.39840.1174-0.1934-0.32440.05880.03990.1184-0.0432-0.11120.1640.06870.3646-20.235642.413645.5525
138.762-8.81033.061413.1448-3.37475.1183-0.1901-0.53180.74020.39370.295-0.5468-0.35420.104-0.1050.101-0.0282-0.12240.0656-0.05980.3853-12.948841.233460.9564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 68
2X-RAY DIFFRACTION2A69 - 128
3X-RAY DIFFRACTION3A129 - 145
4X-RAY DIFFRACTION4A146 - 191
5X-RAY DIFFRACTION5B9 - 21
6X-RAY DIFFRACTION6B22 - 51
7X-RAY DIFFRACTION7B52 - 140
8X-RAY DIFFRACTION8B141 - 189
9X-RAY DIFFRACTION9C34 - 104
10X-RAY DIFFRACTION10C124 - 214
11X-RAY DIFFRACTION11C244 - 255
12X-RAY DIFFRACTION12C256 - 394
13X-RAY DIFFRACTION13C395 - 426

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