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- PDB-4xvy: MycF mycinamicin III 3'-O-methyltransferase in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 4xvy
TitleMycF mycinamicin III 3'-O-methyltransferase in complex with SAH
ComponentsMycinamicin III 3''-O-methyltransferase
KeywordsTRANSFERASE / macrolide / methyltransferase / antibiotic / natural product
Function / homology
Function and homology information


mycinamicin III 3''-O-methyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / small molecule binding / methylation / magnesium ion binding
Similarity search - Function
Macrocin-O-methyltransferase (TylF) / Macrocin-O-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Mycinamicin III 3''-O-methyltransferase
Similarity search - Component
Biological speciesMicromonospora griseorubida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsAkey, D.L. / Smith, J.L.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O-Methyltransferases.
Authors: Bernard, S.M. / Akey, D.L. / Tripathi, A. / Park, S.R. / Konwerski, J.R. / Anzai, Y. / Li, S. / Kato, F. / Sherman, D.H. / Smith, J.L.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycinamicin III 3''-O-methyltransferase
B: Mycinamicin III 3''-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4516
Polymers61,6332
Non-polymers8174
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-32 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.057, 89.892, 127.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 4 - 254 / Label seq-ID: 24 - 274

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F


Mass: 30816.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Plasmid: pET28b-mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293.1 K / Method: vapor diffusion / Details: 20-30% PEG 3350, 100 mM BisTrisPropane pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→43.73 Å / Num. obs: 22837 / % possible obs: 98.4 % / Redundancy: 6.4 % / Rsym value: 0.114 / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVZ

4xvz


Resolution: 2.42→43.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 31.154 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25807 1142 5.1 %RANDOM
Rwork0.20626 ---
obs0.20889 21163 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.565 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--7.49 Å20 Å2
3----5.7 Å2
Refinement stepCycle: LAST / Resolution: 2.42→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 54 35 4029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194088
X-RAY DIFFRACTIONr_bond_other_d0.0040.023752
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9595554
X-RAY DIFFRACTIONr_angle_other_deg0.99838596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33122.981208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1815638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4741540
X-RAY DIFFRACTIONr_chiral_restr0.0840.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214648
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02988
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_it1.4292.1531986
X-RAY DIFFRACTIONr_mcbond_other1.4292.1521985
X-RAY DIFFRACTIONr_mcangle_it2.4083.2142472
X-RAY DIFFRACTIONr_mcangle_other2.4073.2152473
X-RAY DIFFRACTIONr_scbond_it1.6092.3782102
X-RAY DIFFRACTIONr_scbond_other1.6082.3792102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6693.5223083
X-RAY DIFFRACTIONr_long_range_B_refined6.25517.9974829
X-RAY DIFFRACTIONr_long_range_B_other6.255184830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15158 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.42→2.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 61 -
Rwork0.385 1331 -
obs--84.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82732.00790.13842.22440.07195.2305-0.0764-0.18390.0498-0.1592-0.1094-0.0060.3137-0.97340.18580.2166-0.10220.05550.7078-0.020.3052-27.3892-6.447-36.1409
20.4760.11721.09221.0743-0.43223.2414-0.2419-0.04060.0424-0.1917-0.09740.0177-0.3343-0.04040.33940.30990.0227-0.06470.5252-0.02030.4329-16.13724.7846-31.954
31.33450.67831.6641.98061.7029.2110.1389-0.2451-0.4472-0.0628-0.1865-0.18020.3992-0.03260.04760.4793-0.0536-0.07340.2440.12950.4536-11.556-18.7126-21.1554
42.01754.2750.271612.99510.65630.03940.2453-0.044-0.25340.5802-0.20890.20310.0272-0.0088-0.03640.46230.04890.00710.30570.02420.4437-8.6403-10.8625-37.4423
52.4944-0.01542.47060.66120.42014.1715-0.1797-0.0524-0.0162-0.2322-0.05590.0013-0.03660.54390.23560.23220.00730.01250.5940.08340.3684-7.9389-0.5359-31.4807
60.8681-0.01032.08860.0103-0.08145.4017-0.086-0.42410.01990.0043-0.0888-0.0434-0.1423-0.51670.17490.04180.0018-0.01620.99560.04330.3072-16.4849-0.0205-15.5541
70.3433-0.49590.98811.0877-1.02913.30990.00940.06850.07680.0756-0.1509-0.17070.28670.11140.14150.2867-0.02490.03310.6377-0.04310.3591-22.9251-5.6779-54.2096
80.12120.00550.83270.02290.02286.3078-0.1559-0.14270.01550.0067-0.053-0.104-0.6957-1.23760.20880.28570.0687-0.06480.7981-0.01480.5142-34.02945.852-57.8472
93.5060.52871.91650.1254-0.23310.69540.8872-0.2409-0.39040.0530.0115-0.0220.5546-0.3124-0.89880.5595-0.2357-0.0770.3801-0.02460.3414-38.5083-16.841-70.0829
103.07472.2388-1.63662.317-2.54263.5339-0.0348-0.3811-0.1132-0.10920.23750.04890.175-0.7813-0.20270.3543-0.09820.02560.55630.05160.3588-41.7687-10.0428-53.3561
113.0890.22063.5530.8464-0.30284.5491-0.1649-0.46970.1144-0.0186-0.0028-0.0768-0.1232-0.88030.16770.0281-0.0602-0.00011.1493-0.03390.0973-42.3320.6047-58.7047
120.5821-0.33470.93560.31480.16925.845-0.03250.17680.20030.019-0.1531-0.17360.0485-0.23970.18560.0668-0.075400.7980.02540.3756-33.49181.9469-74.4895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 59
2X-RAY DIFFRACTION2A60 - 115
3X-RAY DIFFRACTION3A116 - 143
4X-RAY DIFFRACTION4A144 - 150
5X-RAY DIFFRACTION5A151 - 190
6X-RAY DIFFRACTION6A191 - 254
7X-RAY DIFFRACTION7B4 - 59
8X-RAY DIFFRACTION8B60 - 115
9X-RAY DIFFRACTION9B116 - 143
10X-RAY DIFFRACTION10B144 - 150
11X-RAY DIFFRACTION11B151 - 190
12X-RAY DIFFRACTION12B191 - 254

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