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- PDB-4gf5: Crystal Structure of Calicheamicin Methyltransferase, CalS11 -

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Basic information

Entry
Database: PDB / ID: 4gf5
TitleCrystal Structure of Calicheamicin Methyltransferase, CalS11
ComponentsCalS11
KeywordsTRANSFERASE / CalS11 / SAH / Methyltransferase / Calicheamicin / Structural Genomics / Protein Structure Initiative / PSI / PSI-Biology / NATPRO / Enzyme Discovery for Natural Products Biosynthesis / Center for Eukaryotic Structural Genomics / CESG / Enzyme Discovery for Natural Product Biosynthesis
Function / homology
Function and homology information


O-methyltransferase activity
Similarity search - Function
Methyltransferase domain / Macrocin-O-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / CalS11
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHelmich, K.E. / Singh, S. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: to be published
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalS11
C: CalS11
E: CalS11
F: CalS11
H: CalS11
B: CalS11
D: CalS11
G: CalS11
I: CalS11
J: CalS11
K: CalS11
L: CalS11
M: CalS11
N: CalS11
O: CalS11
P: CalS11
Q: CalS11
R: CalS11
S: CalS11
T: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)589,39568
Polymers579,01720
Non-polymers10,37848
Water49,2532734
1
A: CalS11
C: CalS11
E: CalS11
F: CalS11
H: CalS11
B: CalS11
D: CalS11
G: CalS11
I: CalS11
J: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,69734
Polymers289,50810
Non-polymers5,18924
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58040 Å2
ΔGint-523 kcal/mol
Surface area74960 Å2
MethodPISA
2
K: CalS11
L: CalS11
M: CalS11
N: CalS11
O: CalS11
P: CalS11
Q: CalS11
R: CalS11
S: CalS11
T: CalS11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,69734
Polymers289,50810
Non-polymers5,18924
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58090 Å2
ΔGint-535 kcal/mol
Surface area74830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.112, 106.240, 184.600
Angle α, β, γ (deg.)80.880, 81.650, 70.020
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a decamer. There are 2 biological units in the asymmetric unit (chains A-J and chains K-T)

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Components

#1: Protein
CalS11


Mass: 28950.844 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: AAM70337, calS11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q8KNF1
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2734 / 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: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution (11 mg/ml CalS11, 25mM Tris pH 8.0, 5 mg/ml calicheamicin) mixed in a 1:1 ratio with the well solution (25% PEG 3350, .2M LiSO4, .1M Tris pH 8.5) Cryoprotected with 30% PEG ...Details: Protein solution (11 mg/ml CalS11, 25mM Tris pH 8.0, 5 mg/ml calicheamicin) mixed in a 1:1 ratio with the well solution (25% PEG 3350, .2M LiSO4, .1M Tris pH 8.5) Cryoprotected with 30% PEG 3350, .2M LiSO4, .1M Tris pH 8.5, Vapor diffusion, hanging drop, temperature 298K

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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: Nov 5, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 254196 / Num. obs: 254196 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Χ2: 0.797 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.243.70.48483790.634162.9
2.24-2.283.70.46895790.648170.7
2.28-2.323.60.407114900.651186.4
2.32-2.373.70.359131570.677197.7
2.37-2.4240.367131470.66197.9
2.42-2.4840.32130890.667197.9
2.48-2.5440.295131180.678198
2.54-2.6140.261131820.683198.1
2.61-2.6940.233131870.714198.2
2.69-2.7740.21131450.744198.4
2.77-2.8740.161132300.803198.4
2.87-2.9940.144132010.847198.5
2.99-3.1240.122132310.922198.7
3.12-3.2940.097132060.971198.8
3.29-3.4940.084132530.851198.9
3.49-3.7640.072132850.863199
3.76-4.1440.061132710.887199.2
4.14-4.7440.053133460.992199.4
4.74-5.9740.052133390.981199.5
5.97-503.90.042133610.896199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.32 Å
Translation2.5 Å49.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3TOS

3tos


Resolution: 2.2→49.322 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8689 / SU ML: 0.25 / σ(F): 0 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1899 0.75 %5% selected in thin shells
Rwork0.159 ---
all0.1594 254196 --
obs0.1594 254162 94.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 15.2599 Å2 / Biso min: 1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40116 0 660 2734 43510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741882
X-RAY DIFFRACTIONf_angle_d1.18657201
X-RAY DIFFRACTIONf_chiral_restr0.0746281
X-RAY DIFFRACTIONf_plane_restr0.0057499
X-RAY DIFFRACTIONf_dihedral_angle_d13.11115621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1976-2.25260.2544890.1958120281211763
2.2526-2.31350.26731050.2011150841518979
2.3135-2.38150.30691510.1879185661871798
2.3815-2.45840.26261330.1859186841881798
2.4584-2.54630.24251410.183186171875898
2.5463-2.64820.24691380.1792186731881198
2.6482-2.76870.23851540.1855187451889998
2.7687-2.91470.26081300.1833187101884098
2.9147-3.09730.23951410.1824187841892599
3.0973-3.33640.22311450.1632187761892199
3.3364-3.6720.1751480.1501188451899399
3.672-4.20310.17461390.1284189071904699
4.2031-5.29450.16881440.1221188971904199
5.2945-49.33450.16921410.13951894719088100

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