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- PDB-6zt4: Pentapeptide repeat protein MfpA from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6zt4
TitlePentapeptide repeat protein MfpA from Mycobacterium smegmatis
ComponentsPentapeptide repeat protein MfpA
KeywordsPROTEIN BINDING / PENTAPEPTIDE REPEAT PROTEIN / FLUOROQUINOLONE RESISTANCE / DNA GYRASE / DNA MIMICRY / RIGHT-HANDED QUADRILATERAL BETA-HELIX
Function / homologyPentapeptide repeats (8 copies) / Pentapeptide repeats (9 copies) / Pentapeptide repeat / response to antibiotic / Pentapeptide repeat protein MfpA
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8845
Polymers42,6982
Non-polymers1863
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-6 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.006, 85.731, 66.336
Angle α, β, γ (deg.)90.000, 92.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 10 - 188 / Label seq-ID: 11 - 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / 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 PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→66.28 Å / Num. obs: 33772 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 8.9
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
1.77-1.814.41.517838919010.5070.8091.7290.997.1
9.03-66.286.30.04417212730.9990.0180.04827.499.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BM4

2bm4


Resolution: 1.77→52.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.472 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1697 5 %RANDOM
Rwork0.2079 ---
obs0.2092 32049 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.9 Å2 / Biso mean: 33.017 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å21.68 Å2
2--2.69 Å20 Å2
3----4.27 Å2
Refinement stepCycle: final / Resolution: 1.77→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 12 167 3011
Biso mean--46.97 40.14 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132954
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172731
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6434004
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5836254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.9319.11191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.371542
X-RAY DIFFRACTIONr_chiral_restr0.0660.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
Refine LS restraints NCS

Ens-ID: 1 / Number: 5656 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 114 -
Rwork0.392 2344 -
all-2458 -
obs--97.5 %
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)
13.1064.07922.75016.70161.92636.89750.2531-0.61060.19780.3355-0.50650.31990.5965-0.27370.25340.2480.00760.00150.36890.0260.2021-5.8403-19.377158.4585
22.08360.5584-1.08712.7224-1.58254.2412-0.0091-0.06340.0128-0.096-0.12930.0490.38410.04380.13840.0628-0.0012-0.04840.0076-0.00350.1958-3.3293-9.921346.2359
36.34211.2391.94241.87160.17626.7679-0.07890.0294-0.1182-0.1059-0.07660.12760.4520.27670.15550.09450.0702-0.01140.08630.04110.14183.9253-6.7133.1478
41.78970.7123-3.29312.14590.65588.5959-0.033-0.0763-0.0209-0.1262-0.0564-0.06270.09820.30150.08940.09780.0677-0.0430.08290.04270.19226.5815-0.573225.3311
510.8716-1.1484-1.47460.75410.39750.3243-0.11710.87660.0049-0.74190.1439-0.1439-0.3559-0.1057-0.02671.1343-0.04680.15450.46780.04610.267415.555121.0519-24.0647
63.8529-1.37820.16384.94742.04754.82990.45430.38390.2624-0.7071-0.1408-0.2607-1.6364-0.1758-0.31350.70720.07540.09120.06960.07770.202316.219315.1358-17.9497
71.9503-0.7175-2.02332.65520.41446.9040.2116-0.02930.0687-0.2038-0.0508-0.1069-0.9831-0.2169-0.16080.2260.0308-0.03230.04720.01770.205212.35319.407-5.406
82.0263-0.2773-2.18911.84410.54048.8921-0.0150.03650.0192-0.02370.0618-0.0159-0.38390.0238-0.04690.07220.0286-0.05340.05690.02470.196310.08436.549510.2202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 25
2X-RAY DIFFRACTION2A26 - 131
3X-RAY DIFFRACTION3A132 - 145
4X-RAY DIFFRACTION4A146 - 189
5X-RAY DIFFRACTION5B10 - 25
6X-RAY DIFFRACTION6B26 - 76
7X-RAY DIFFRACTION7B77 - 133
8X-RAY DIFFRACTION8B134 - 190

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