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- PDB-1q0z: Crystal structure of aclacinomycin methylesterase (RdmC) with bou... -

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Basic information

Entry
Database: PDB / ID: 1q0z
TitleCrystal structure of aclacinomycin methylesterase (RdmC) with bound product analogue, 10-decarboxymethylaclacinomycin A (DcmA)
Componentsaclacinomycin methylesterase
KeywordsHYDROLASE / Anthracycline / methylesterase / polyketide / Streptomyces / tailoring enzyme / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


aclacinomycin methylesterase / aclacinomycin T methylesterase activity / glycerolipid catabolic process / triacylglycerol lipase activity / antibiotic biosynthetic process
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-DECARBOXYMETHYLACLACINOMYCIN A (DCMAA) / Aclacinomycin methylesterase RdmC
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsJansson, A. / Niemi, J. / Mantsala, P. / Schneider, G. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of aclacinomycin methylesterase with bound product analogues: implications for anthracycline recognition and mechanism.
Authors: Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray diffraction studies of aclacinomycin-10-methyl esterase and aclacinomycin-10-hydroxylase from Streptomyces purpurascens
Authors: Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: aclacinomycin methylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9174
Polymers31,8291
Non-polymers1,0883
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.106, 84.875, 44.389
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein aclacinomycin methylesterase / RdmC


Mass: 31828.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmc / Plasmid: pRDM*12 / Species (production host): Streptomyces lividans / Production host: Streptomyces lividans TK24 (bacteria) / Strain (production host): TK24 / References: UniProt: Q54528
#2: Chemical ChemComp-AKA / 10-DECARBOXYMETHYLACLACINOMYCIN A (DCMAA) / 10-{4-DIMETHYLAMINO-5-[4-HYDROXY-6-METHYL-5-(6-METHYL-5-OXO-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRANE-2-YLOXY]-6-METH YL-TETRAHYDRO-PYRAN-2-YLOXY}-8-ETHYL-1,8,11-TRIHYDROXY-7,8,9,10-TETRAHYDRO-NAPHTHACENE-5,12-DIONE


Mass: 753.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H51NO13
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: Ammonium sulphate, PEG400, Hepes buffer, pH 7.5, VAPOR DIFFUSION, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 mMAcmA1drop
210 mg/mlprotein1drop
350 mMTris-HCl1drop
41 mMdithiothreitol1drop
5ammonium sulfate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.95→26.31 Å / Num. all: 19636 / Num. obs: 19636 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.106 / Net I/σ(I): 15
Reflection shellResolution: 1.95→2.06 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.413 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 95945 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.413

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
REFMAC5refinement
RefinementMethod to determine structure: MIR
Starting model: PDB code 1Q0R, another RdmC+substrate complex

1q0r


Resolution: 1.95→26.31 Å
Isotropic thermal model: Individual isotropic B-factors for each atom
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum likelihood / Details: Riding hydrogens
RfactorNum. reflectionSelection details
Rfree0.185 1538 Random
Rwork0.157 --
all0.159 19234 -
obs0.159 19234 -
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.95→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 75 255 2573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.294
LS refinement shellResolution: 1.95→2.05 Å /
RfactorNum. reflection
Rfree0.21 101
Rwork0.19 -
obs-1264
Refinement
*PLUS
% reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.294

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