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- PDB-7d41: Crystal structure of type III polyketide synthase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 7d41
TitleCrystal structure of type III polyketide synthase from Mycobacterium marinum - P 21 21 21 Space group
Components
  • Chalcone synthase-like protein
  • Chalcone/stilbene synthase
KeywordsTRANSFERASE / Bacterial / TypeIII polyketide synthase / Orthrombic form
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
OCTANOIC ACID (CAPRYLIC ACID) / Chalcone/stilbene synthase
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 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
DepositionSep 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
B: Chalcone synthase-like protein
A: Chalcone/stilbene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4704
Polymers89,1812
Non-polymers2882
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-2 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.732, 99.518, 126.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 27 - 392 / Label seq-ID: 27 - 392

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Chalcone synthase-like protein


Mass: 44547.609 Da / Num. of mol.: 1
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: Protein Chalcone/stilbene synthase


Mass: 44633.652 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M Potassium Sodium tartrate 200 mM Sodium chloride 100 mM Imidazole; pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97735 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97735 Å / Relative weight: 1
ReflectionResolution: 2.419→78.264 Å / Num. obs: 19645 / % possible obs: 92.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 55.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 9.4
Reflection shellResolution: 2.419→2.685 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 983 / CC1/2: 0.719 / Rpim(I) all: 0.419 / Rrim(I) all: 0.752 / % possible all: 57

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
STARANISOdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CB3

7cb3


Resolution: 2.419→78.264 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.087 / SU ML: 0.277 / Cross valid method: FREE R-VALUE / ESU R Free: 0.384
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2582 962 4.897 %
Rwork0.2038 18682 -
all0.206 --
obs-19644 71.027 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.119 Å2-0 Å2-0 Å2
2---0.027 Å20 Å2
3---0.145 Å2
Refinement stepCycle: LAST / Resolution: 2.419→78.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 20 32 5434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175284
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.6317496
X-RAY DIFFRACTIONr_angle_other_deg1.1711.57112082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26421.349252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35915826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6541541
X-RAY DIFFRACTIONr_chiral_restr0.0480.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.1920.2927
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.24822
X-RAY DIFFRACTIONr_nbtor_refined0.1520.22682
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.211
X-RAY DIFFRACTIONr_nbd_other0.2520.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.25
X-RAY DIFFRACTIONr_mcbond_it2.2815.4662925
X-RAY DIFFRACTIONr_mcbond_other2.2815.4672924
X-RAY DIFFRACTIONr_mcangle_it3.7228.2013651
X-RAY DIFFRACTIONr_mcangle_other3.7218.2013652
X-RAY DIFFRACTIONr_scbond_it2.7365.8322573
X-RAY DIFFRACTIONr_scbond_other2.7355.8332574
X-RAY DIFFRACTIONr_scangle_it4.4658.6233845
X-RAY DIFFRACTIONr_scangle_other4.4648.6233846
X-RAY DIFFRACTIONr_lrange_it8.332105.32822465
X-RAY DIFFRACTIONr_lrange_other8.331105.3322465
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.0510591
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.083240.05008
11AX-RAY DIFFRACTIONLocal ncs0.083240.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.419-2.4810.31450.315710.31519980.6590.6493.80380.324
2.481-2.5490.27860.2961560.29619690.6490.7288.22750.291
2.549-2.6230.298130.3193040.31818960.8230.77216.71940.317
2.623-2.7040.349320.3335620.33418490.6880.76732.12550.323
2.704-2.7920.361560.3148830.31618120.8010.79651.82120.296
2.792-2.890.367720.29612630.317250.8080.81377.39130.275
2.89-2.9990.289870.27414430.27516900.8260.83990.53250.252
2.999-3.1210.327660.24315440.24716270.840.86698.95510.222
3.121-3.260.271760.23214850.23415610.8870.8981000.208
3.26-3.4190.28720.22314240.22514960.8940.9141000.204
3.419-3.6030.257610.19913570.20114180.9140.9391000.184
3.603-3.8210.222560.18913080.19113660.930.94399.85360.177
3.821-4.0850.228520.17212230.17412770.9350.95299.84340.167
4.085-4.4110.233520.15611350.15911870.9480.9621000.161
4.411-4.830.226480.14710570.1511070.9510.96799.81930.16
4.83-5.3980.254440.1819600.18410070.9420.95399.70210.196
5.398-6.2280.286430.2418640.2439070.9210.9281000.261
6.228-7.6160.308510.2087220.2147730.90.9431000.242
7.616-10.720.187470.1675710.1696180.9670.9711000.2
10.72-78.2640.256230.2593500.2593740.9340.93999.73260.356

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