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- PDB-1r00: Crystal structure of aclacinomycin-10-hydroxylase (RdmB) in compl... -

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Basic information

Entry
Database: PDB / ID: 1r00
TitleCrystal structure of aclacinomycin-10-hydroxylase (RdmB) in complex with S-adenosyl-L-homocysteine (SAH)
Componentsaclacinomycin-10-hydroxylase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Anthracycline / hydroxylase / methyltransferase / polyketide / Streptomyces / tailoring enzyme
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / protein dimerization activity
Similarity search - Function
Helix Hairpins - #1350 / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins ...Helix Hairpins - #1350 / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / 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
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / fft / Resolution: 2.5 Å
AuthorsJansson, A. / Niemi, J. / Lindqvist, Y. / Mantsala, P. / Schneider, G.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Aclacinomycin-10-Hydroxylase, a S-Adenosyl-L-Methionine-dependent Methyltransferase Homolog Involved in Anthracycline Biosynthesis in Streptomyces purpurascens.
Authors: Jansson, A. / Niemi, J. / Lindqvist, Y. / Mantsala, P. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray diffraction studies of aclacinomycin-10-methylesterase and aclacinomycin-10-hydroxylase from Streptomyces purpurascens
Authors: Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G.
History
DepositionSep 19, 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: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2018Group: Advisory / Data collection / Structure summary
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct
Item: _diffrn_source.pdbx_synchrotron_site / _struct.title
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: aclacinomycin-10-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2813
Polymers39,8381
Non-polymers4432
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: aclacinomycin-10-hydroxylase
hetero molecules

A: aclacinomycin-10-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5636
Polymers79,6762
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7910 Å2
ΔGint-55 kcal/mol
Surface area28360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.120, 92.130, 115.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein aclacinomycin-10-hydroxylase / RdmB


Mass: 39837.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmb / Plasmid: pRDM16 / Production host: Escherichia coli (E. coli) / Strain (production host): XL2-blue / References: UniProt: Q54527
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, ammonium acetate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG40001reservoir
20.1 Mammonium acetate1reservoir
30.2 Msodium acetate1reservoirpH5.0
42.2 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 12651 / Num. obs: 12651 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.108 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.252 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 96318 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: fft
Starting model: PDB entry 1QZZ, SAM-complex

1qzz


Resolution: 2.5→30 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; the occupancy is put to zero on the sidechains of Gln15, Asp57, Lys84, Glu219, Arg298, Arg319
RfactorNum. reflectionSelection details
Rfree0.28 7680 random
Rwork0.213 --
all0.218 12560 -
obs0.218 12560 -
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 30 91 2691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg1.395
LS refinement shellResolution: 2.5→2.59 Å /
RfactorNum. reflection
Rfree0.329 75
Rwork0.241 -
obs-829
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.011
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.395

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