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- PDB-2f99: Crystal structure of the polyketide cyclase AknH with bound subst... -

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Basic information

Entry
Database: PDB / ID: 2f99
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-AKV / : / Aklanonic acid methyl ester cyclase AcmA
Similarity search - Component
Biological speciesStreptomyces galilaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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_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)74,51919
Polymers71,8054
Non-polymers2,71415
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Aklanonic Acid methyl Ester Cyclase, AknH
D: Aklanonic Acid methyl Ester Cyclase, AknH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,30710
Polymers35,9022
Non-polymers1,4058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-103 kcal/mol
Surface area12400 Å2
MethodPISA
3
A: Aklanonic Acid methyl Ester Cyclase, AknH
B: Aklanonic Acid methyl Ester Cyclase, AknH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2119
Polymers35,9022
Non-polymers1,3097
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-89 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.740, 151.740, 108.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
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.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AKV / {3-[(1R,3S)-1,3-DIHYDROXYPENTYL]-4,5,9,10-TETRAHYDROXY-2-ANTHRYL}ACETATE / DERIVATIVE OF AKLANONIC ACID METHYL ESTER (AAME)


Mass: 414.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H22O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2004
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→84.52 Å / Num. all: 73655 / Num. obs: 73655 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.056 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.95 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F98

2f98


Resolution: 1.9→84.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.744 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20679 3713 5 %RANDOM
Rwork0.18536 ---
obs0.18644 69906 99.96 %-
all-73655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.095 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.37 Å20 Å2
2---0.73 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 175 459 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214989
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9696778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79122.952271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0051550
X-RAY DIFFRACTIONr_chiral_restr0.0890.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023900
X-RAY DIFFRACTIONr_nbd_refined0.2080.22291
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2432
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2170
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.280
X-RAY DIFFRACTIONr_mcbond_it0.5521.52886
X-RAY DIFFRACTIONr_mcangle_it0.90624534
X-RAY DIFFRACTIONr_scbond_it1.3332763
X-RAY DIFFRACTIONr_scangle_it2.2474.52244
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 277 -
Rwork0.203 5137 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1000000000000000000000000
21.0501-0.0998-0.30011.677-0.2940.72930.07430.16920.1922-0.1268-0.044-0.0041-0.05110.007-0.0303-0.0315-0.00060.002-0.0780.0436-0.078116.958732.67140.12
31.4834-0.02040.35981.49640.00430.8012-0.0107-0.2691-0.12160.39090.06880.2119-0.0183-0.1738-0.05810.02060.01780.1071-0.06920.0457-0.093771.634813.997663.2002
40.6714-0.097-0.21461.46770.15440.4601-0.0026-0.0014-0.1068-0.0551-0.0306-0.0490.07810.01440.0332-0.0608-0.0028-0.0022-0.07510.0108-0.043818.99942.41418.0973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 14011 - 149
2X-RAY DIFFRACTION2BB2 - 14011 - 149
3X-RAY DIFFRACTION3CC2 - 14011 - 149
4X-RAY DIFFRACTION4DD2 - 14011 - 149

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