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- PDB-3gxo: Structure of the Mitomycin 7-O-methyltransferase MmcR with bound ... -

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Basic information

Entry
Database: PDB / ID: 3gxo
TitleStructure of the Mitomycin 7-O-methyltransferase MmcR with bound Mitomycin A
ComponentsMmcR
KeywordsTRANSFERASE / Methyltransferase / Mitomycin / MmcR / S-adenosyl methionine
Function / homology
Function and homology information


mitomycin 6-O-methyltransferase / quinone biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MQA / S-ADENOSYL-L-HOMOCYSTEINE / Mitomycin biosynthesis 6-O-methyltransferase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSingh, S. / Chang, A. / Bingman, C.A. / Phillips Jr., G.N. / Thorson, J.S.
CitationJournal: Proteins / Year: 2011
Title: Structural characterization of the mitomycin 7-O-methyltransferase.
Authors: Singh, S. / Chang, A. / Goff, R.D. / Bingman, C.A. / Gruschow, S. / Sherman, D.H. / Phillips, G.N. / Thorson, J.S.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MmcR
D: MmcR
C: MmcR
B: MmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,31214
Polymers160,2974
Non-polymers3,01510
Water5,927329
1
A: MmcR
B: MmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6166
Polymers80,1492
Non-polymers1,4684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-47 kcal/mol
Surface area25950 Å2
MethodPISA
2
D: MmcR
C: MmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6968
Polymers80,1492
Non-polymers1,5486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-56 kcal/mol
Surface area25900 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.841, 98.844, 171.045
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
MmcR


Mass: 40074.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: mmcR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9X5T6
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#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.: 4 / Source method: obtained synthetically / Formula: C16H19N3O6
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 mg/ml MmcR Protein, 0.05 M NaCl, 0.02 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0) Crystals were soaked ...Details: Protein Solution (10 mg/ml MmcR Protein, 0.05 M NaCl, 0.02 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0) Crystals were soaked with 5mM Mitomycin A for 8hrs Cryoprotected with 25% ethylene glycol, 10% PEG4K, 15% MPD, 0.1 M CaCl2, 0.1 M MES pH 6.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2008 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 59548 / % possible obs: 88.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.332
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.383.30.3153.861170.7
2.38-2.483.40.276174.7
2.48-2.593.50.244178.5
2.59-2.733.60.217182
2.73-2.93.70.169187.7
2.9-3.123.70.149195.1
3.12-3.443.90.118199.2
3.44-3.934.10.086199.6
3.93-4.954.40.066199.8
4.95-504.40.048199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.58 Å43.92 Å
Translation2.58 Å43.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GWZ

3gwz


Resolution: 2.3→43.92 Å / Occupancy max: 1 / Occupancy min: 0.05 / SU ML: 0.19 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 3003 5.05 %
Rwork0.202 --
obs0.205 59450 88.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.32 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 36.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.716 Å2-0 Å2-0 Å2
2---1.072 Å20 Å2
3----2.711 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 206 329 10831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710752
X-RAY DIFFRACTIONf_angle_d1.10214679
X-RAY DIFFRACTIONf_dihedral_angle_d18.3453905
X-RAY DIFFRACTIONf_chiral_restr0.0611695
X-RAY DIFFRACTIONf_plane_restr0.0051917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3360.2981220.2352059X-RAY DIFFRACTION70
2.336-2.3770.3291060.252161X-RAY DIFFRACTION71
2.377-2.420.3151140.2452176X-RAY DIFFRACTION73
2.42-2.4670.311100.2222246X-RAY DIFFRACTION75
2.467-2.5170.3131230.2312321X-RAY DIFFRACTION77
2.517-2.5720.3141290.2222365X-RAY DIFFRACTION80
2.572-2.6310.2931440.2182399X-RAY DIFFRACTION80
2.631-2.6970.291460.2142456X-RAY DIFFRACTION82
2.697-2.770.2811190.2112523X-RAY DIFFRACTION84
2.77-2.8520.3121400.2142641X-RAY DIFFRACTION88
2.852-2.9440.3171340.2112768X-RAY DIFFRACTION91
2.944-3.0490.2931540.2192846X-RAY DIFFRACTION95
3.049-3.1710.2651430.222978X-RAY DIFFRACTION99
3.171-3.3150.251660.2193005X-RAY DIFFRACTION99
3.315-3.490.2551440.1993039X-RAY DIFFRACTION100
3.49-3.7080.2441830.1952979X-RAY DIFFRACTION100
3.708-3.9940.2331660.1843040X-RAY DIFFRACTION100
3.994-4.3960.2141610.1643054X-RAY DIFFRACTION100
4.396-5.0310.21520.1733070X-RAY DIFFRACTION100
5.031-6.3360.231630.2113114X-RAY DIFFRACTION100
6.336-43.9290.2211840.1813207X-RAY DIFFRACTION99

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