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

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Basic information

Entry
Database: PDB / ID: 1qzz
TitleCrystal structure of aclacinomycin-10-hydroxylase (RdmB) in complex with S-adenosyl-L-methionine (SAM)
Componentsaclacinomycin-10-hydroxylase
KeywordsOXIDOREDUCTASE / TRANSFERASE / Anthracycline / hydroxylase / methyltransferase / polyketide / Streptomyces / tailoring enzymes / Structural Proteomics in Europe / SPINE / Structural Genomics
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-ADENOSYLMETHIONINE / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJansson, A. / Niemi, J. / Lindqvist, Y. / Mantsala, P. / Schneider, G. / Structural Proteomics in Europe (SPINE)
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 / Structure summary / Category: pdbx_unobs_or_zero_occ_atoms / struct / Item: _struct.title
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _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-10-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2953
Polymers39,8381
Non-polymers4572
Water4,792266
1


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

A: aclacinomycin-10-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5916
Polymers79,6762
Non-polymers9154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7630 Å2
ΔGint-56 kcal/mol
Surface area28410 Å2
MethodPISA
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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2

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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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1110.8439
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9778, 0.9781, 0.9116
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 23, 2001
MARRESEARCH2CCDAug 5, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.84391
20.97781
30.97811
40.91161
ReflectionResolution: 2.1→30 Å / Num. all: 19452 / Num. obs: 19452 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.069 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.355 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 67648 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 92.5 % / Rmerge(I) obs: 0.355

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→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
Rfree0.275 5380 Random
Rwork0.204 --
all0.21 19414 -
obs0.21 19414 -
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 31 266 2867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg1.372
LS refinement shellResolution: 2.1→2.16 Å
RfactorNum. reflection
Rfree0.283 103
Rwork0.237 -
obs-1104
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.009
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.372

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