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- PDB-5hoq: Apo structure of CalS11, TDP-rhamnose 3'-o-methyltransferase, an ... -

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Basic information

Entry
Database: PDB / ID: 5hoq
TitleApo structure of CalS11, TDP-rhamnose 3'-o-methyltransferase, an enzyme in Calicheamicin biosynthesis
ComponentsTDP-rhamnose 3'-O-methyltransferase (CalS11)
KeywordsTRANSFERASE / rhamnose methyltransferase Calicheamicin biosynthesis
Function / homologyMethyltransferase domain / Macrocin-O-methyltransferase / O-methyltransferase activity / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CalS11
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.793 Å
AuthorsHan, L. / Helmich, K.E. / Singh, S. / Thorson, J.S. / Bingman, C.A. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis
CitationJournal: Struct Dyn. / Year: 2016
Title: Loop dynamics of thymidine diphosphate-rhamnose 3'-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis.
Authors: Han, L. / Singh, S. / Thorson, J.S. / Phillips, G.N.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMar 30, 2016ID: 4PWR
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TDP-rhamnose 3'-O-methyltransferase (CalS11)
B: TDP-rhamnose 3'-O-methyltransferase (CalS11)
C: TDP-rhamnose 3'-O-methyltransferase (CalS11)
D: TDP-rhamnose 3'-O-methyltransferase (CalS11)
E: TDP-rhamnose 3'-O-methyltransferase (CalS11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23510
Polymers144,7545
Non-polymers4805
Water31,4541746
1
A: TDP-rhamnose 3'-O-methyltransferase (CalS11)
B: TDP-rhamnose 3'-O-methyltransferase (CalS11)
C: TDP-rhamnose 3'-O-methyltransferase (CalS11)
D: TDP-rhamnose 3'-O-methyltransferase (CalS11)
E: TDP-rhamnose 3'-O-methyltransferase (CalS11)
hetero molecules

A: TDP-rhamnose 3'-O-methyltransferase (CalS11)
B: TDP-rhamnose 3'-O-methyltransferase (CalS11)
C: TDP-rhamnose 3'-O-methyltransferase (CalS11)
D: TDP-rhamnose 3'-O-methyltransferase (CalS11)
E: TDP-rhamnose 3'-O-methyltransferase (CalS11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,46920
Polymers289,50810
Non-polymers96110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area56770 Å2
ΔGint-480 kcal/mol
Surface area76200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.262, 125.142, 107.152
Angle α, β, γ (deg.)90.00, 125.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-786-

HOH

21D-733-

HOH

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Components

#1: Protein
TDP-rhamnose 3'-O-methyltransferase (CalS11)


Mass: 28950.844 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KNF1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1746 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1:1 ratio mixture of 16mg/ml protein and reservoir solution (21% PEG3350, 0.1M LiSO4, 0.1M HEPES pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.793→47.888 Å / Num. obs: 147725 / % possible obs: 99 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1316 / Net I/σ(I): 10.25
Reflection shellResolution: 1.793→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 1.39 / % possible all: 90

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDS20151015data reduction
XDS20151015data scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GF5

4gf5


Resolution: 1.793→47.888 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 7387 5 %
Rwork0.1461 --
obs0.1477 131836 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.793→47.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 25 1746 11055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099668
X-RAY DIFFRACTIONf_angle_d1.00613176
X-RAY DIFFRACTIONf_dihedral_angle_d13.5985808
X-RAY DIFFRACTIONf_chiral_restr0.1361453
X-RAY DIFFRACTIONf_plane_restr0.0071730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7932-1.81360.35163210.3396035X-RAY DIFFRACTION65
1.8136-1.83490.31994940.29399423X-RAY DIFFRACTION100
1.8349-1.85730.29784840.28099252X-RAY DIFFRACTION100
1.8573-1.88080.28394960.26849388X-RAY DIFFRACTION100
1.8808-1.90560.26834930.25819425X-RAY DIFFRACTION100
1.9056-1.93170.28434880.23669243X-RAY DIFFRACTION100
1.9317-1.95930.24124960.22579384X-RAY DIFFRACTION100
1.9593-1.98850.26074960.22299389X-RAY DIFFRACTION100
1.9885-2.01960.23794950.20599368X-RAY DIFFRACTION100
2.0196-2.05270.22154860.19049337X-RAY DIFFRACTION100
2.0527-2.08810.22084980.18529365X-RAY DIFFRACTION100
2.0881-2.12610.22944880.18349324X-RAY DIFFRACTION100
2.1261-2.1670.19564960.1739388X-RAY DIFFRACTION100
2.167-2.21120.20984910.16439325X-RAY DIFFRACTION100
2.2112-2.25930.18224880.15119358X-RAY DIFFRACTION100
2.2593-2.31180.17874990.14559418X-RAY DIFFRACTION100
2.3118-2.36960.16884910.13249273X-RAY DIFFRACTION100
2.3696-2.43370.17684850.13619358X-RAY DIFFRACTION100
2.4337-2.50530.1784900.13039311X-RAY DIFFRACTION100
2.5053-2.58620.17764930.13149358X-RAY DIFFRACTION100
2.5862-2.67860.17744980.13549325X-RAY DIFFRACTION100
2.6786-2.78580.16834940.12859437X-RAY DIFFRACTION100
2.7858-2.91260.16064920.12789274X-RAY DIFFRACTION100
2.9126-3.06620.19234920.13889387X-RAY DIFFRACTION100
3.0662-3.25820.16555000.13379347X-RAY DIFFRACTION100
3.2582-3.50970.18344900.12839346X-RAY DIFFRACTION100
3.5097-3.86280.15534900.12789371X-RAY DIFFRACTION100
3.8628-4.42140.14194880.10569347X-RAY DIFFRACTION100
4.4214-5.56910.1214940.10139344X-RAY DIFFRACTION100
5.5691-47.90530.16134940.14629324X-RAY DIFFRACTION100
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)
10.7528-0.1111-0.13860.4187-0.07560.4426-0.0313-0.2124-0.14660.09340.01190.06390.1132-0.00060.00920.25930.00210.01660.23470.05020.1636-8.5584-54.345122.577
20.6576-0.1102-0.00920.43480.15720.53970.0103-0.26170.25310.10920.0124-0.1431-0.01950.1388-0.04210.1912-0.0138-0.02890.2768-0.12050.229122.0372-20.808624.5364
30.5464-0.02140.02620.4324-0.0720.43840.0474-0.04070.45170.03930.02150.0437-0.1574-0.0783-0.05250.2330.03730.04150.1734-0.0110.5108-14.12041.3823.0905
40.7858-0.0309-0.17250.55260.02260.44-0.0332-0.1759-0.12120.08510.0392-0.12350.0940.0905-0.00920.19880.0512-0.01530.1920.02770.164518.7186-54.949612.6917
50.6966-0.0128-0.00460.34870.13160.39950.0413-0.34180.24180.14990.01470.0748-0.00470.0145-0.03160.24350.00420.02470.3217-0.13040.2213-5.618-18.918232.299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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