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- PDB-1sjw: Structure of polyketide cyclase SnoaL -

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Basic information

Entry
Database: PDB / ID: 1sjw
TitleStructure of polyketide cyclase SnoaL
Componentsnogalonic acid methyl ester cyclase
KeywordsLYASE / Anthracyclines / Nogalamycin / SnoaL / aldol condensation / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


nogalonic acid methyl ester cyclase / polyketide metabolic process / antibiotic biosynthetic process / isomerase activity
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 / Nogalonic acid methyl ester cyclase
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.35 Å
AuthorsSultana, A. / Kallio, P. / Jansson, A. / Wang, J.S. / Neimi, J. / Mantsala, P. / Schneider, G. / Structural Proteomics in Europe (SPINE)
Citation
Journal: Embo J. / Year: 2004
Title: Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.
Authors: Sultana, A. / Kallio, P. / Jansson, A. / Wang, J.S. / Niemi, J. / Schneider, G.
#1: Journal: To be Published
Title: Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis
Authors: Sultana, A. / Kallio, P. / Jansson, A. / Neimi, J. / Mantsala, P. / Schneider, G.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site
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 / pdbx_struct_special_symmetry / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHORS STATE THAT THE SNOAL GENE STARTS EARLIER THAN PREDICTED FROM THE ORIGINALLY ...SEQUENCE THE AUTHORS STATE THAT THE SNOAL GENE STARTS EARLIER THAN PREDICTED FROM THE ORIGINALLY DEPOSITED SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nogalonic acid methyl ester cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1672
Polymers16,7891
Non-polymers3781
Water2,252125
1
A: nogalonic acid methyl ester cyclase
hetero molecules

A: nogalonic acid methyl ester cyclase
hetero molecules

A: nogalonic acid methyl ester cyclase
hetero molecules

A: nogalonic acid methyl ester cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6698
Polymers67,1564
Non-polymers1,5134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
2
A: nogalonic acid methyl ester cyclase
hetero molecules

A: nogalonic acid methyl ester cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3344
Polymers33,5782
Non-polymers7572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5220 Å2
ΔGint-22 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.10, 72.00, 65.40
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

21A-385-

HOH

31A-422-

HOH

41A-431-

HOH

DetailsThe biological assembly is a tetramer generated from the one monomer in the assymetric unit by the operations (-1,-1,0),(-1,0,-1),(0,-1,-1).

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Components

#1: Protein nogalonic acid methyl ester cyclase


Mass: 16788.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: SnoaL / Plasmid: pBAD/hisB / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q9RN59
#2: 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.: 1 / Source method: obtained synthetically / Formula: C21H14O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.16 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Tris HCl, Na Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONMAX II I71121.099
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDApr 14, 2003
BRUKER SMART 10002CCDNov 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.0991
ReflectionResolution: 1.35→36.03 Å / Num. obs: 35447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 16.57 Å2 / Rsym value: 0.085 / Net I/σ(I): 23.3
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.485 / % possible all: 98.5

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Processing

Software
NameVersionClassification
SHELXLrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: SIRAS
Starting model: Built by ARP/WARP

Resolution: 1.35→36.03 Å / Num. parameters: 12538 / Num. restraintsaints: 15347 / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY SHELX
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2764 -Random
Rwork0.143 ---
all-35948 --
obs-35447 95.72 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-1.14 Å21.58 Å2
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1101 / Occupancy sum non hydrogen: 1347.25
Refinement stepCycle: LAST / Resolution: 1.35→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 28 125 1322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.15
LS refinement shellResolution: 1.35→36.03 Å
RfactorNum. reflection% reflection
Rfree0.176 2764 -
Rwork0.143 --
obs-402458 95.72 %

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