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- PDB-5j6o: Crystal structure of a trans-AT PKS dehydratase domain of C0ZGQ7 ... -

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Basic information

Entry
Database: PDB / ID: 5j6o
TitleCrystal structure of a trans-AT PKS dehydratase domain of C0ZGQ7 from Brevibacillus brevis
ComponentsPutative polyketide synthase
KeywordsLYASE / polyketide / trans-AT / PKS
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.195 Å
AuthorsJakob, R.P. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: Crystal Structures of Dehydratase Domains from trans-AT Polyketide Biosynthetic Pathway
Authors: Jakob, R.P. / Herbst, D.A. / Muller, R. / Maier, T.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4222
Polymers35,3981
Non-polymers241
Water905
1
A: Putative polyketide synthase
hetero molecules

A: Putative polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8444
Polymers70,7962
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 63.500, 145.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-2301-

MG

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Components

#1: Protein Putative polyketide synthase /


Mass: 35397.941 Da / Num. of mol.: 1 / Fragment: UNP residues 1922-2240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (strain 47 / JCM 6285 / NBRC 100599) (bacteria)
Strain: 47 / JCM 6285 / NBRC 100599 / Gene: BBR47_39890 / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0ZGQ7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG20000, 20% PEG550MME, 0.1 M Mops/Hepes pH 7.5, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.195→47.8 Å / Num. obs: 5296 / % possible obs: 95.5 % / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.6
Reflection shellResolution: 3.195→3.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.2 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2131: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG9

3kg9


Resolution: 3.195→47.8 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.82
RfactorNum. reflection% reflection
Rfree0.3062 549 10.37 %
Rwork0.2716 --
obs0.2753 5296 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.195→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 1 5 2170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072208
X-RAY DIFFRACTIONf_angle_d1.1492993
X-RAY DIFFRACTIONf_dihedral_angle_d11.5841813
X-RAY DIFFRACTIONf_chiral_restr0.059338
X-RAY DIFFRACTIONf_plane_restr0.01390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1952-3.51670.46881400.33411112X-RAY DIFFRACTION97
3.5167-4.02530.34761310.28281167X-RAY DIFFRACTION100
4.0253-5.07060.25071200.25621202X-RAY DIFFRACTION99
5.0706-47.8050.29621580.26751266X-RAY DIFFRACTION99

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