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- PDB-4hzp: The Structure of the Bifunctional Acetyltransferase/Decarboxylase... -

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Basic information

Entry
Database: PDB / ID: 4hzp
TitleThe Structure of the Bifunctional Acetyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double Hot Dog Fold
ComponentsBifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
KeywordsTRANSFERASE / LYASE / Structural Genomics / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology / Double Hot Dog Fold / Acyl Carrier Protein - LnmL / methylmalonyl-CoA
Function / homology
Function and homology information


S-acyltransferase activity
Similarity search - Function
LnmK, N-terminal / LnmK N-terminal Hot Dog Fold domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Conserved hypthetical protein
Similarity search - Component
Biological speciesStreptomyces atroolivaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLohman, J.R. / Bingman, C.A. / Phillips Jr., G.N. / Shen, B. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Biochemistry / Year: 2013
Title: Structure of the Bifunctional Acyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double-Hot-Dog Fold.
Authors: Lohman, J.R. / Bingman, C.A. / Phillips, G.N. / Shen, B.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 20, 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: Bifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2585
Polymers35,2631
Non-polymers9954
Water2,882160
1
A: Bifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules

A: Bifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,51710
Polymers70,5272
Non-polymers1,9908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6160 Å2
ΔGint-96 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.711, 59.711, 311.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

DetailsThe biological dimer is generated by the symmetry mate: x, x-y, -z+1/6

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Components

#1: Protein Bifunctional methylmalonyl-CoA:ACP Acyltransferase/Decarboxylase


Mass: 35263.285 Da / Num. of mol.: 1 / Mutation: T2S, Y62F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atroolivaceus (bacteria) / Gene: LnmK / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GGP1
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 20 mg/mL in 100 mM NaCl and 10 mM Tris-HCl, pH 8.0 plus 10 mM methylmalonyl-CoA. Precipitant: 20 - 23% MEPEG 2000, 0.25-0.35 M (NH4)2SO4 and 0.1 M Bis-tris propane-HCl, pH 7.0 in 4 ...Details: Protein: 20 mg/mL in 100 mM NaCl and 10 mM Tris-HCl, pH 8.0 plus 10 mM methylmalonyl-CoA. Precipitant: 20 - 23% MEPEG 2000, 0.25-0.35 M (NH4)2SO4 and 0.1 M Bis-tris propane-HCl, pH 7.0 in 4 L drops (1:1, protein:well). , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. all: 33385 / Num. obs: 32885 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4HZN

4hzn


Resolution: 1.77→29.72 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.366 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27477 1656 5.1 %RANDOM
Rwork0.2249 ---
obs0.2274 30964 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.185 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.77→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 37 160 2532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9693296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45622.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6215367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8741530
X-RAY DIFFRACTIONr_chiral_restr0.140.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211888
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.51480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00122385
X-RAY DIFFRACTIONr_scbond_it3.0323941
X-RAY DIFFRACTIONr_scangle_it4.6444.5911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.773→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 125 -
Rwork0.294 2185 -
obs--97.22 %

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