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- PDB-8zc8: The structure of MitM and mitomycin A with SAH in mitomycin -

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Basic information

Entry
Database: PDB / ID: 8zc8
TitleThe structure of MitM and mitomycin A with SAH in mitomycin
ComponentsMitM
KeywordsTRANSFERASE / SAM-dependent methyltransferase
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / : / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-MQA / S-ADENOSYL-L-HOMOCYSTEINE / MitM
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

Downloads & links

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Assembly

Deposited unit
A: MitM
B: MitM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2895
Polymers62,1702
Non-polymers1,1183
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.953, 113.953, 108.771
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: 31085.221 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) / Gene: mitM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X5Q9
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MQA / [(1aS,8S,8aR,8bS)-6,8a-dimethoxy-5-methyl-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazireno[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate / Mitomycin A


Mass: 349.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% w/v PEG 3350, 10% w/v Ethylene glycol, 0.2 M Sodium sulfate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97861 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.8→49.34 Å / Num. obs: 20544 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2957 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT11.29data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZC7

8zc7


Resolution: 2.8→49.34 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2001 9.75 %
Rwork0.2239 --
obs0.2258 20514 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 77 4 4212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134294
X-RAY DIFFRACTIONf_angle_d1.4725844
X-RAY DIFFRACTIONf_dihedral_angle_d16.8451538
X-RAY DIFFRACTIONf_chiral_restr0.065659
X-RAY DIFFRACTIONf_plane_restr0.026775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.40591430.41321316X-RAY DIFFRACTION100
2.87-2.950.40991390.36521291X-RAY DIFFRACTION100
2.95-3.030.38411390.33591308X-RAY DIFFRACTION100
3.03-3.130.33871410.34041299X-RAY DIFFRACTION100
3.13-3.240.31561440.32851294X-RAY DIFFRACTION100
3.24-3.370.36251430.31991325X-RAY DIFFRACTION100
3.37-3.530.30631390.29511306X-RAY DIFFRACTION100
3.53-3.710.31371410.25371317X-RAY DIFFRACTION100
3.71-3.950.26791440.23661321X-RAY DIFFRACTION100
3.95-4.250.22061420.21011309X-RAY DIFFRACTION100
4.25-4.680.21171460.16921318X-RAY DIFFRACTION100
4.68-5.350.1981460.17531339X-RAY DIFFRACTION100
5.35-6.740.17861450.20321350X-RAY DIFFRACTION100
6.74-49.340.18311490.16261420X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 52.3638 Å / Origin y: -6.2356 Å / Origin z: 9.3857 Å
111213212223313233
T0.793 Å2-0.0631 Å20.0864 Å2-0.4723 Å2-0.1322 Å2--0.6156 Å2
L1.5938 °20.7232 °2-0.6619 °2-0.8137 °2-0.7608 °2--0.941 °2
S0.2408 Å °-0.1899 Å °0.2327 Å °0.364 Å °-0.0434 Å °0.1542 Å °-0.2833 Å °0.1582 Å °-0.1717 Å °
Refinement TLS groupSelection details: all

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