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- PDB-3gwz: Structure of the Mitomycin 7-O-methyltransferase MmcR -

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Basic information

Entry
Database: PDB / ID: 3gwz
TitleStructure of the Mitomycin 7-O-methyltransferase MmcR
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
S-ADENOSYL-L-HOMOCYSTEINE / Mitomycin biosynthesis 6-O-methyltransferase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / SAD / Resolution: 1.91 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 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,46816
Polymers160,2974
Non-polymers2,17112
Water15,691871
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MmcR
B: MmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1947
Polymers80,1492
Non-polymers1,0455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-84 kcal/mol
Surface area26020 Å2
MethodPISA
3
D: MmcR
C: MmcR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2749
Polymers80,1492
Non-polymers1,1257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-103 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.372, 98.918, 171.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
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) Cryoprotected with 25% ...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) 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, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97945,0.96421
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.964211
ReflectionResolution: 1.91→50 Å / Num. obs: 115235 / % possible obs: 98.6 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.113 / Χ2: 1.03 / Net I/σ(I): 11.545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.91-1.989.20.572.428101690.96987.9
1.98-2.0612.20.477113661.00298.1
2.06-2.1513.20.361114901.04599.6
2.15-2.2613.60.278115951.00499.9
2.26-2.41140.217115871.03499.9
2.41-2.5914.30.175116221.055100
2.59-2.8514.50.138116981.08100
2.85-3.2714.90.095116931.028100
3.27-4.11150.075118050.986100
4.11-5014.60.055122101.064100

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.91 Å / Lowest resolution: 43.13 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_1001066038489
ANO_10.8370.9771053830
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_18.4-43.13001109421
ISO_15.99-8.4002091427
ISO_14.91-5.99002749428
ISO_14.26-4.91003332439
ISO_13.81-4.26003767425
ISO_13.48-3.81004179441
ISO_13.23-3.48004598432
ISO_13.02-3.23004922432
ISO_12.85-3.02005219431
ISO_12.7-2.85005590434
ISO_12.58-2.7005867439
ISO_12.47-2.58006105424
ISO_12.37-2.47006448438
ISO_12.28-2.37006661428
ISO_12.21-2.28006905430
ISO_12.14-2.21007176434
ISO_12.07-2.14007373415
ISO_12.02-2.07007558412
ISO_11.96-2.02007646402
ISO_11.91-1.96007308357
ANO_18.4-43.130.4243.01411090
ANO_15.99-8.40.3953.32720910
ANO_14.91-5.990.4383.02127490
ANO_14.26-4.910.5572.38733320
ANO_13.81-4.260.5972.15937670
ANO_13.48-3.810.6112.02441790
ANO_13.23-3.480.6361.86745980
ANO_13.02-3.230.6291.75149220
ANO_12.85-3.020.6811.55552190
ANO_12.7-2.850.7461.30755900
ANO_12.58-2.70.7891.09558670
ANO_12.47-2.580.8350.92861050
ANO_12.37-2.470.8730.80664460
ANO_12.28-2.370.9070.6666570
ANO_12.21-2.280.9330.56668950
ANO_12.14-2.210.9510.4971570
ANO_12.07-2.140.9610.43772880
ANO_12.02-2.070.9750.38573870
ANO_11.96-2.020.980.36573250
ANO_11.91-1.960.990.35367000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-3.711-97.509-30.375SE31.041.72
2-9.16-70.873-70.627SE24.581.69
3-3.427-35.955-148.955SE25.251.75
4-22.285-4.342-14.001SE26.881.67
5-15.659-56.025-82.281SE15.31.32
6-11.39-10.854-43.823SE18.781.4
7-19.231-10.662-86.624SE20.561.39
8-13.475-54.377-84.694SE23.491.16
9-12.496-47.334-135.261SE19.041.22
10-10.951-50.475-132.217SE39.771.37
11-15.941-12.212-86.005SE38.311.24
12-7.631-94.768-45.338SE48.381.48
13-12.706-70.783-85.717SE33.231.09
14-15.958-94.469-84.592SE34.91.18
15-4.87-33.998-133.496SE39.831.08
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 115091
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.36-10068.70.676831
7.33-10.3662.60.9041424
5.98-7.3360.90.8921824
5.18-5.9861.70.8992106
4.63-5.1856.50.9222402
4.23-4.6357.30.9272614
3.92-4.2358.90.9262844
3.66-3.9261.10.9193021
3.45-3.6658.60.9173252
3.28-3.4561.60.9113362
3.12-3.2861.80.9053589
2.99-3.1261.50.9033737
2.87-2.9962.90.8983861
2.77-2.8764.50.9014028
2.68-2.7764.50.8994119
2.59-2.6866.50.8934354
2.51-2.5966.90.8994422
2.44-2.5168.70.9024556
2.38-2.4469.60.8984652
2.32-2.3871.10.8954848
2.26-2.3274.20.8984902
2.21-2.2675.40.8974978
2.16-2.2175.10.8955212
2.12-2.1677.40.8935257
2.07-2.1278.90.895341
2.03-2.0781.20.8855446
1.99-2.0380.90.8755472
1.96-1.9983.80.855452
1.91-1.96840.797185

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.91→19.653 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.23 / σ(F): 1.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 5763 5.01 %
Rwork0.174 --
obs0.176 114971 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.348 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 85.92 Å2 / Biso mean: 23.386 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.051 Å20 Å2-0 Å2
2--0.037 Å20 Å2
3----0.081 Å2
Refinement stepCycle: LAST / Resolution: 1.91→19.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10296 0 140 871 11307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610762
X-RAY DIFFRACTIONf_angle_d114679
X-RAY DIFFRACTIONf_chiral_restr0.0641690
X-RAY DIFFRACTIONf_plane_restr0.0041934
X-RAY DIFFRACTIONf_dihedral_angle_d16.1813901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.9340.3331600.2533142330287
1.934-1.9570.271710.2263402357393
1.957-1.980.271760.2053505368196
1.98-2.0060.2541720.2053556372897
2.006-2.0320.2751900.1913533372399
2.032-2.060.2372090.1873643385299
2.06-2.0890.2581860.1873596378299
2.089-2.120.2491730.18636523825100
2.12-2.1530.2661810.17836553836100
2.153-2.1890.2361860.17136453831100
2.189-2.2260.1981970.17136333830100
2.226-2.2670.2331860.1836843870100
2.267-2.310.2352000.17336163816100
2.31-2.3570.2481860.1736763862100
2.357-2.4080.2231860.17136853871100
2.408-2.4640.2041890.16936283817100
2.464-2.5260.2162120.16636373849100
2.526-2.5940.2112160.16636363852100
2.594-2.670.2061950.17136823877100
2.67-2.7560.2352140.17236493863100
2.756-2.8550.231710.17936953866100
2.855-2.9680.2172230.17736453868100
2.968-3.1030.2251740.17637113885100
3.103-3.2660.2151910.17637063897100
3.266-3.470.1861960.16636903886100
3.47-3.7360.1811910.15737273918100
3.736-4.1090.172170.1537023919100
4.109-4.6960.1552130.1437443957100
4.696-5.890.1952150.17537763991100
5.89-19.6540.1691870.16939574144100

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