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- PDB-8zc7: Crystallographic analysis of MitM, which catalyzes the post-mitos... -

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Basic information

Entry
Database: PDB / ID: 8zc7
TitleCrystallographic analysis of MitM, which catalyzes the post-mitosane modification in mitomycin biosynthesis
ComponentsMitM
KeywordsTRANSFERASE / SAM-dependent methyltransferase
Function / homologyPolyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / : / Methyltransferase type 11 / Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / MitM
Function and homology information
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsXia, M. / Dong, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303100 China
CitationJournal: To Be Published
Title: Crystallographic analysis of MitM, which catalyzes the post-mitosane modification in mitomycin biosynthesis
Authors: Xia, M. / Dong, D.
History
DepositionApr 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MitM
B: MitM


Theoretical massNumber of molelcules
Total (without water)63,8282
Polymers63,8282
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-8 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.357, 113.357, 110.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein MitM


Mass: 31914.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Streptomyces caespitosus is not available, replaced by Q9X5Q9 temporarily.
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Strain: ATCC 27422 / Gene: mitM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X5Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane, PH 6.5, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97891 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.23→49.36 Å / Num. obs: 23376 / % possible obs: 99.2 % / Redundancy: 10.5 % / CC1/2: 0.998 / Net I/σ(I): 8.6
Reflection shellResolution: 2.23→2.29 Å / Num. unique obs: 23376 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACT3.27data extraction
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→31.366 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 1992 8.52 %
Rwork0.1997 --
obs0.2042 23376 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→31.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 0 35 4142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124187
X-RAY DIFFRACTIONf_angle_d1.4975673
X-RAY DIFFRACTIONf_dihedral_angle_d23.2291551
X-RAY DIFFRACTIONf_chiral_restr0.297631
X-RAY DIFFRACTIONf_plane_restr0.009757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6601-2.72660.38661450.33941532X-RAY DIFFRACTION99
2.7266-2.80030.2951440.26041518X-RAY DIFFRACTION100
2.8003-2.88260.32941480.23931558X-RAY DIFFRACTION100
2.8826-2.97560.29171460.23231547X-RAY DIFFRACTION100
2.9756-3.08190.30651450.22491516X-RAY DIFFRACTION100
3.0819-3.20510.26111460.21471559X-RAY DIFFRACTION100
3.2051-3.35080.33971440.21861542X-RAY DIFFRACTION100
3.3508-3.52730.27141420.23441554X-RAY DIFFRACTION100
3.5273-3.74790.2851190.21351314X-RAY DIFFRACTION84
3.7479-4.03680.22861260.19891342X-RAY DIFFRACTION87
4.0368-4.4420.25531450.17411556X-RAY DIFFRACTION100
4.442-5.08240.21651450.16011589X-RAY DIFFRACTION100
5.0824-6.39440.25691490.2041593X-RAY DIFFRACTION100
6.3944-31.360.19021480.17221664X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 52.5281 Å / Origin y: -6.202 Å / Origin z: 9.6761 Å
111213212223313233
T0.4476 Å2-0.0645 Å20.0466 Å2-0.2936 Å2-0.0699 Å2--0.3282 Å2
L1.5198 °20.6646 °2-0.7349 °2-0.7162 °2-0.6017 °2--0.8119 °2
S0.151 Å °-0.1999 Å °0.1339 Å °0.1861 Å °-0.0569 Å °0.1141 Å °-0.1674 Å °0.1252 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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