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- PDB-1xdu: Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in compl... -

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Basic information

Entry
Database: PDB / ID: 1xdu
TitleCrystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with Sinefungin (SFG)
ComponentsProtein RdmB
KeywordsTRANSFERASE / Anthracycline / hydroxylase / S-adenosyl-L-methionine analogue / sinefungin / streptomyces / polyketide antibiotics / divergent evolution
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / O-methyltransferase activity / carboxy-lyase activity / antibiotic biosynthetic process
Similarity search - Function
Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / 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 ...Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / 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 / SINEFUNGIN / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJansson, A. / Koskiniemi, H. / Erola, A. / Wang, J. / Mantsala, P. / Schneider, G. / Niemi, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Aclacinomycin 10-Hydroxylase Is a Novel Substrate-assisted Hydroxylase Requiring S-Adenosyl-L-methionine as Cofactor
Authors: Jansson, A. / Koskiniemi, H. / Erola, A. / Wang, J. / Schneider, G. / Niemi, J.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Protein RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6073
Polymers40,1661
Non-polymers4402
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein RdmB
hetero molecules

A: Protein RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2136
Polymers80,3322
Non-polymers8814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7380 Å2
ΔGint-57 kcal/mol
Surface area28910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.758, 86.813, 117.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein Protein RdmB


Mass: 40166.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmb / Plasmid: pRDM16 from pGEX4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54527
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.17 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium acetate, PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.7→58.7 Å / Num. all: 8940 / Num. obs: 8940 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.82 % / Biso Wilson estimate: 40 Å2 / Rsym value: 0.104 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.252 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RdmB+SAM complex

Resolution: 2.7→58.72 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.854 / SU B: 16.587 / SU ML: 0.343 / Isotropic thermal model: Isotropic B-factors for each atom / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29513 419 4.7 %RANDOM
Rwork0.22742 ---
obs0.23059 8521 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.176 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--2.08 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.7→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 31 26 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212631
X-RAY DIFFRACTIONr_bond_other_d0.0020.022497
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9883580
X-RAY DIFFRACTIONr_angle_other_deg0.81835719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165337
X-RAY DIFFRACTIONr_chiral_restr0.0590.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02562
X-RAY DIFFRACTIONr_nbd_refined0.2040.2619
X-RAY DIFFRACTIONr_nbd_other0.2260.22829
X-RAY DIFFRACTIONr_nbtor_other0.0810.21599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.2128
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.27
X-RAY DIFFRACTIONr_mcbond_it0.5111.51689
X-RAY DIFFRACTIONr_mcangle_it0.97322676
X-RAY DIFFRACTIONr_scbond_it0.9893942
X-RAY DIFFRACTIONr_scangle_it1.8524.5904
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.426 30
Rwork0.264 614

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