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- PDB-8byr: Crystal structure of MoaB2 protein from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 8byr
TitleCrystal structure of MoaB2 protein from Mycobacterium smegmatis
ComponentsMolybdopterin biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / Sigma factor binding protein
Function / homology: / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Mo-molybdopterin cofactor biosynthetic process / Molybdopterin biosynthesis protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsNarasimhan, S. / Sanderova, H. / Zidek, L. / Krasny, L.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA19-12956S Czech Republic
CitationJournal: J.Bacteriol. / Year: 2024
Title: MoaB2, a newly identified transcription factor, binds to sigma A in Mycobacterium smegmatis.
Authors: Brezovska, B. / Narasimhan, S. / Sikova, M. / Sanderova, H. / Koval, T. / Borah, N. / Shoman, M. / Pospisilova, D. / Vankova Hausnerova, V. / Tuzincin, D. / Cerny, M. / Komarek, J. / ...Authors: Brezovska, B. / Narasimhan, S. / Sikova, M. / Sanderova, H. / Koval, T. / Borah, N. / Shoman, M. / Pospisilova, D. / Vankova Hausnerova, V. / Tuzincin, D. / Cerny, M. / Komarek, J. / Janouskova, M. / Kambova, M. / Halada, P. / Krenkova, A. / Hubalek, M. / Trundova, M. / Dohnalek, J. / Hnilicova, J. / Zidek, L. / Krasny, L.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdopterin biosynthesis protein
B: Molybdopterin biosynthesis protein
C: Molybdopterin biosynthesis protein
D: Molybdopterin biosynthesis protein
E: Molybdopterin biosynthesis protein
F: Molybdopterin biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)105,7316
Polymers105,7316
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration, The expected size is around 100KDa, and the GF elution volume was around 77KDa(Due to the presence of trimers and hexamers)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.295, 105.560, 106.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Molybdopterin biosynthesis protein


Mass: 17621.857 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria)
Strain: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis)
Gene: MSMEG_5485 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0R3I5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium chloride, 14% w/v PEG 400, 0.1M sodium-HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Nov 9, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.53→47.69 Å / Num. obs: 35068 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Χ2: 0.99 / Net I/σ(I): 15 / Num. measured all: 470613
Reflection shellResolution: 2.53→2.64 Å / % possible obs: 99.5 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.868 / Num. measured all: 56564 / Num. unique obs: 4206 / CC1/2: 0.872 / Rpim(I) all: 0.242 / Rrim(I) all: 0.902 / Χ2: 0.98 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
AimlessVersion 0.7.4data scaling
XDSXDS-GUI (GPL V2)data reduction
MOLREPVersion 11.0 /22.07.2010/phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFQ

3rfq


Resolution: 2.53→47.69 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.207 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1827 5.2 %RANDOM
Rwork0.19187 ---
obs0.19547 33188 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.53→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 0 101 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166408
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6168570
X-RAY DIFFRACTIONr_angle_other_deg0.4991.55714624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.495883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.141559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23910989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021259
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_it4.4934.8643568
X-RAY DIFFRACTIONr_mcbond_other4.4924.8643568
X-RAY DIFFRACTIONr_mcangle_it6.468.7314439
X-RAY DIFFRACTIONr_mcangle_other6.4598.7324440
X-RAY DIFFRACTIONr_scbond_it5.2485.4432730
X-RAY DIFFRACTIONr_scbond_other5.2475.4432731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7859.8044132
X-RAY DIFFRACTIONr_long_range_B_refined9.38244.056514
X-RAY DIFFRACTIONr_long_range_B_other9.38243.846513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.532→2.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 136 -
Rwork0.313 2408 -
obs--99.65 %

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