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- PDB-5kku: Crystal structure of an N-terminal dehydratase from difficidin as... -

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Basic information

Entry
Database: PDB / ID: 5kku
TitleCrystal structure of an N-terminal dehydratase from difficidin assembly line
ComponentsPolyketide synthase type I
KeywordsLYASE / dehydratase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase / Polyketide synthase dehydratase N-terminal domain / 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 / Thiol Ester Dehydrase; Chain A / Polyketide synthase, phosphopantetheine-binding domain ...Polyketide synthase dehydratase / Polyketide synthase dehydratase N-terminal domain / 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 / Thiol Ester Dehydrase; Chain A / 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 / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyketide synthase type I
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKeatinge-Clay, A.T. / Zeng, J.
CitationJournal: To Be Published
Title: A Dehydratase Provides Insights into Split Bimodules and Polypeptide Docking in trans-AT Polyketide Synthases
Authors: Zeng, J. / Keatinge-Clay, A.T.
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.type
Revision 1.2Sep 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
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: Polyketide synthase type I
B: Polyketide synthase type I
C: Polyketide synthase type I
D: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)138,6654
Polymers138,6654
Non-polymers00
Water362
1
A: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)34,6661
Polymers34,6661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)34,6661
Polymers34,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)34,6661
Polymers34,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)34,6661
Polymers34,6661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.355, 73.981, 94.178
Angle α, β, γ (deg.)90.20, 90.08, 90.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Polyketide synthase type I


Mass: 34666.258 Da / Num. of mol.: 4 / Fragment: UNP residues 1-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: difJ
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q1RS44
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG4000, 0.2 M Lithium Sulfate, 0.1 M Tris-HCl (pH 8.5)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.03322 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.22→39.786 Å / Num. obs: 49121 / % possible obs: 89.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.469
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.488 / % possible all: 61.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20003.15data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN9

4ln9


Resolution: 2.22→39.786 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 2512 5.12 %RANDOM
Rwork0.2171 ---
obs0.2187 49098 89.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→39.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 0 2 9353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0329571
X-RAY DIFFRACTIONf_angle_d2.47812915
X-RAY DIFFRACTIONf_dihedral_angle_d16.8823588
X-RAY DIFFRACTIONf_chiral_restr0.1881384
X-RAY DIFFRACTIONf_plane_restr0.0131674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2201-2.26280.3361030.29191611X-RAY DIFFRACTION56
2.2628-2.3090.33911200.28411951X-RAY DIFFRACTION66
2.309-2.35920.2953820.26122060X-RAY DIFFRACTION71
2.3592-2.41410.29421300.26542233X-RAY DIFFRACTION77
2.4141-2.47450.291310.26532384X-RAY DIFFRACTION81
2.4745-2.54140.30671380.26042477X-RAY DIFFRACTION85
2.5414-2.61610.3091140.26952622X-RAY DIFFRACTION90
2.6161-2.70060.30971290.26452708X-RAY DIFFRACTION93
2.7006-2.79710.31311400.27492780X-RAY DIFFRACTION96
2.7971-2.9090.29611630.26692840X-RAY DIFFRACTION98
2.909-3.04140.26971560.25452847X-RAY DIFFRACTION98
3.0414-3.20160.26211680.2412862X-RAY DIFFRACTION99
3.2016-3.40210.26881470.22982870X-RAY DIFFRACTION98
3.4021-3.66460.24561380.20022869X-RAY DIFFRACTION99
3.6646-4.03310.21251710.18542860X-RAY DIFFRACTION99
4.0331-4.6160.19111580.15532890X-RAY DIFFRACTION99
4.616-5.81270.18021650.16312868X-RAY DIFFRACTION99
5.8127-39.79240.2161590.18432854X-RAY DIFFRACTION99

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