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- PDB-2f98: Crystal structure of the polyketide cyclase AknH with bound subst... -

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Basic information

Entry
Database: PDB / ID: 2f98
TitleCrystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity.
ComponentsAklanonic Acid methyl Ester Cyclase, AknH
KeywordsBIOSYNTHETIC PROTEIN / anthracycline / polyketide cyclase / stereoselectivity / aklavinone
Function / homology
Function and homology information


aklanonic acid methyl ester cyclase / daunorubicin biosynthetic process / intramolecular lyase activity / doxorubicin metabolic process / antibiotic biosynthetic process
Similarity search - Function
SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-NGV / : / Aklanonic acid methyl ester cyclase AcmA
Similarity search - Component
Biological speciesStreptomyces galilaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKallio, P. / Sultana, A. / Neimi, J. / Mantsala, P. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity.
Authors: Kallio, P. / Sultana, A. / Niemi, J. / Schneider, G.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Aklanonic Acid methyl Ester Cyclase, AknH
B: Aklanonic Acid methyl Ester Cyclase, AknH
C: Aklanonic Acid methyl Ester Cyclase, AknH
D: Aklanonic Acid methyl Ester Cyclase, AknH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,70212
Polymers71,8054
Non-polymers1,8988
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.271, 152.271, 109.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARG2AA2 - 911 - 18
21SERSERARGARG2BB2 - 911 - 18
31SERSERARGARG2CC2 - 911 - 18
41SERSERARGARG2DD2 - 911 - 18
52TYRTYRPROPRO2AA31 - 4540 - 54
62TYRTYRPROPRO2BB31 - 4540 - 54
72TYRTYRPROPRO2CC31 - 4540 - 54
82TYRTYRPROPRO2DD31 - 4540 - 54
93LEULEUVALVAL4AA47 - 5556 - 64
103LEULEUVALVAL4BB47 - 5556 - 64
113LEULEUVALVAL4CC47 - 5556 - 64
123LEULEUVALVAL4DD47 - 5556 - 64
134LYSLYSGLUGLU4AA57 - 6166 - 70
144LYSLYSGLUGLU4BB57 - 6166 - 70
154LYSLYSGLUGLU4CC57 - 6166 - 70
164LYSLYSGLUGLU4DD57 - 6166 - 70
175LEULEUILEILE4AA65 - 7074 - 79
185LEULEUILEILE4BB65 - 7074 - 79
195LEULEUILEILE4CC65 - 7074 - 79
205LEULEUILEILE4DD65 - 7074 - 79
216GLUGLUGLUGLU4AA72 - 14081 - 149
226GLUGLUGLUGLU4BB72 - 14081 - 149
236GLUGLUGLUGLU4CC72 - 14081 - 149
246GLUGLUGLUGLU4DD72 - 14081 - 149
257ALAALAPROPRO4AA14 - 2923 - 38
267ALAALAPROPRO4BB14 - 2923 - 38
277ALAALAPROPRO4CC14 - 2923 - 38
287ALAALAPROPRO4DD14 - 2923 - 38
DetailsBiological assembly is a tetramer. There are also four molecules in the assymetric unit which forms tetramer by generating the symmetric molecules with the symmetry operator 0,-1,-1 and 1,0,-1

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Components

#1: Protein
Aklanonic Acid methyl Ester Cyclase, AknH


Mass: 17951.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces galilaeus (bacteria) / Plasmid: pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: GenBank: 7800671, UniProt: O52646*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NGV / METHYL 5,7-DIHYDROXY-2-METHYL-4,6,11-TRIOXO-3,4,6,11-TETRAHYDROTETRACENE-1-CARBOXYLATE / NOGALAVIKETONE


Mass: 378.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H14O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0M ammonium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 27, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→56.48 Å / Num. all: 55241 / Num. obs: 55241 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SJW

1sjw


Resolution: 2.1→56.48 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.592 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21838 2804 5.1 %RANDOM
Rwork0.19342 ---
obs0.19469 52433 100 %-
all-55241 --
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: 29.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0.41 Å20 Å2
2---0.82 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 132 245 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214969
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9586751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375561
X-RAY DIFFRACTIONr_chiral_restr0.0850.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026
X-RAY DIFFRACTIONr_nbd_refined0.2040.22138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.252
X-RAY DIFFRACTIONr_mcbond_it0.551.52801
X-RAY DIFFRACTIONr_mcangle_it1.0324526
X-RAY DIFFRACTIONr_scbond_it1.51732168
X-RAY DIFFRACTIONr_scangle_it2.4514.52225
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A92tight positional0.040.05
2B92tight positional0.040.05
3C92tight positional0.040.05
4D92tight positional0.040.05
1A955medium positional0.190.5
2B955medium positional0.160.5
3C955medium positional0.20.5
4D955medium positional0.160.5
1A92tight thermal0.250.5
2B92tight thermal0.170.5
3C92tight thermal0.220.5
4D92tight thermal0.30.5
1A955medium thermal1.272
2B955medium thermal0.932
3C955medium thermal1.382
4D955medium thermal1.52
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 205
Rwork0.222 3927

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