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- PDB-4pne: Crystal Structure of the [4+2]-Cyclase SpnF -

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Basic information

Entry
Database: PDB / ID: 4pne
TitleCrystal Structure of the [4+2]-Cyclase SpnF
ComponentsMethyltransferase-like protein
KeywordsBIOSYNTHETIC PROTEIN / Cyclase / SAM-dependent methyltransferase-like / Spinosyn synthesis / TRANSFERASE
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase-like protein
Similarity search - Component
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsFage, C.D. / Isiorho, E.A. / Liu, Y.-N. / Liu, H.-W. / Keatinge-Clay, A.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM35906 United States
Welch FoundationF-1712 United States
Welch FoundationF-1511 United States
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: The structure of SpnF, a standalone enzyme that catalyzes [4 + 2] cycloaddition.
Authors: Fage, C.D. / Isiorho, E.A. / Liu, Y. / Wagner, D.T. / Liu, H.W. / Keatinge-Clay, A.T.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase-like protein
B: Methyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2096
Polymers65,2362
Non-polymers9734
Water3,999222
1
A: Methyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1043
Polymers32,6181
Non-polymers4862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1043
Polymers32,6181
Non-polymers4862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint1 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.740, 69.350, 83.630
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyltransferase-like protein


Mass: 32617.863 Da / Num. of mol.: 2 / Fragment: UNP residues 2-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnF / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ALM7
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.84 Å3/Da / Density % sol: 33.14 % / Description: Plate-like crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium sulfate, 2% v/v PEG 400, 10 mM HEPES pH 7.5, 100 mM sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionNumber: 273979 / Rmerge(I) obs: 0.112 / Χ2: 0.95 / D res high: 1.5 Å / Num. obs: 74158 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
1.51.54544310.964
1.541.58527210.776
1.581.63520010.713
1.631.68500310.619
1.681.73488110.561
1.731.79471910.488
1.791.86455310.43
1.861.94442410.378
1.942.02423710.296
2.022.12401510.22
2.122.24386810.169
2.242.37362610.142
2.372.54343910.118
2.542.74317310.092
2.743294110.069
33.35263710.055
3.353.87233910.043
3.874.74196310.04
4.746.71155910.04
ReflectionResolution: 1.5→82.497 Å / Num. obs: 74158 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.695 % / Biso Wilson estimate: 14.53 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.19
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 1.56 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.17 Å41.51 Å
Translation2.17 Å41.51 Å

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
XDS2.5.2data scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BUS

3bus


Resolution: 1.5→82.92 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3719 5.02 %Random selection
Rwork0.197 ---
obs0.198 74131 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.76 Å2
Refinement stepCycle: LAST / Resolution: 1.5→82.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 66 222 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114296
X-RAY DIFFRACTIONf_angle_d1.3735839
X-RAY DIFFRACTIONf_dihedral_angle_d13.8571569
X-RAY DIFFRACTIONf_chiral_restr0.056643
X-RAY DIFFRACTIONf_plane_restr0.007770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51890.33181240.28782578X-RAY DIFFRACTION98
1.5189-1.53890.29261530.28032585X-RAY DIFFRACTION97
1.5389-1.560.30661440.26352567X-RAY DIFFRACTION98
1.56-1.58230.27871130.24492600X-RAY DIFFRACTION98
1.5823-1.60590.28191240.25262624X-RAY DIFFRACTION98
1.6059-1.6310.30441300.2492553X-RAY DIFFRACTION98
1.631-1.65780.32621330.24552604X-RAY DIFFRACTION97
1.6578-1.68630.2731450.23092585X-RAY DIFFRACTION98
1.6863-1.7170.2771400.22452605X-RAY DIFFRACTION98
1.717-1.750.26021400.22732620X-RAY DIFFRACTION98
1.75-1.78580.24281380.21662570X-RAY DIFFRACTION98
1.7858-1.82460.27261210.21662634X-RAY DIFFRACTION98
1.8246-1.8670.26911380.20322626X-RAY DIFFRACTION98
1.867-1.91370.24371410.21252597X-RAY DIFFRACTION98
1.9137-1.96550.23531400.19442655X-RAY DIFFRACTION99
1.9655-2.02330.19591350.19592589X-RAY DIFFRACTION99
2.0233-2.08860.20731410.19852631X-RAY DIFFRACTION98
2.0886-2.16330.23451360.17682604X-RAY DIFFRACTION99
2.1633-2.24990.21411430.18762622X-RAY DIFFRACTION98
2.2499-2.35230.26741220.18712620X-RAY DIFFRACTION98
2.3523-2.47630.2391490.18782622X-RAY DIFFRACTION98
2.4763-2.63150.19611340.19172614X-RAY DIFFRACTION98
2.6315-2.83470.19231310.19572622X-RAY DIFFRACTION98
2.8347-3.120.2161700.19372590X-RAY DIFFRACTION98
3.12-3.57140.20781350.18652590X-RAY DIFFRACTION97
3.5714-4.49960.16571600.16492625X-RAY DIFFRACTION98
4.4996-83.04410.17861390.17992680X-RAY DIFFRACTION98

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