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- PDB-7cb3: Crystal structure of type III polyketide synthase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 7cb3
TitleCrystal structure of type III polyketide synthase from Mycobacterium marinum
ComponentsChalcone/stilbene synthase
KeywordsTRANSFERASE / Bacterial / TypeIII polyketide synthase
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
ACETATE ION / MYRISTIC ACID / TRIETHYLENE GLYCOL / Chalcone/stilbene synthase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPratap, S. / Kant, A. / Saxena, P. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)CRG/2018/002229 India
CitationJournal: To Be Published
Title: Crystal structure of type III polyketide synthase from Mycobacterium marinum.
Authors: Pratap, S. / Kant, A. / Saxena, P. / Krishnan, V.
History
DepositionJun 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone/stilbene synthase
B: Chalcone/stilbene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2029
Polymers89,2672
Non-polymers9347
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint6 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.407, 131.407, 187.187
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 30 - 392 / Label seq-ID: 30 - 392

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Chalcone/stilbene synthase


Mass: 44633.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_2190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HNE1
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) Polyethylene glycol 3000 and 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.306→72.287 Å / Num. obs: 28212 / % possible obs: 90.4 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.027 / Rrim(I) all: 0.064 / Net I/σ(I): 17.9
Reflection shellResolution: 2.306→2.487 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1411 / CC1/2: 0.576 / Rpim(I) all: 0.487 / Rrim(I) all: 0.747 / % possible all: 68

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TED

1ted


Resolution: 2.31→72.287 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 17.221 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21743 1552 5.5 %RANDOM
Rwork0.19787 ---
obs0.19896 26660 53.05 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.669 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----3.9 Å2
Refinement stepCycle: 1 / Resolution: 2.31→72.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 64 76 5403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195412
X-RAY DIFFRACTIONr_bond_other_d0.0020.025059
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9727372
X-RAY DIFFRACTIONr_angle_other_deg0.973311636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76324.1200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27515780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9271533
X-RAY DIFFRACTIONr_chiral_restr0.0830.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216137
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021040
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_it1.43.3112905
X-RAY DIFFRACTIONr_mcbond_other1.3863.3082901
X-RAY DIFFRACTIONr_mcangle_it2.2954.9633624
X-RAY DIFFRACTIONr_mcangle_other2.2954.9633625
X-RAY DIFFRACTIONr_scbond_it1.7183.5212507
X-RAY DIFFRACTIONr_scbond_other1.7183.5222508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7415.1933749
X-RAY DIFFRACTIONr_long_range_B_refined5.71963.03522585
X-RAY DIFFRACTIONr_long_range_B_other5.71963.03722586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 22154 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.31→2.365 Å
RfactorNum. reflection% reflection
Rfree0.344 8 -
Rwork0.38 194 -
obs--5.15 %
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)
15.64230.527-0.2442.8063-0.16570.549-0.04850.05670.483-0.09410.0475-0.0977-0.06940.04320.00090.02-0.0098-0.00560.00580.00220.1374-22.09767.7712.384
25.71190.4630.27032.77990.08590.5484-0.04390.0296-0.4339-0.06360.04310.13880.0595-0.06860.00080.019-0.0115-0.01390.01060.00210.1418-43.59246.0692.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 392
2X-RAY DIFFRACTION2B30 - 392

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