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- PDB-5e1v: Crystal structure of a monomeric dehydratase domain from a trans ... -

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Basic information

Entry
Database: PDB / ID: 5e1v
TitleCrystal structure of a monomeric dehydratase domain from a trans AT polyketide synthase split module
ComponentsPolyketide synthase PksL
KeywordsOXIDOREDUCTASE / dehydratase / polyketide synthase / bacillaene
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / cytoplasm
Similarity search - Function
Polyketide synthase dehydratase / : / Prismane-like superfamily / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain ...Polyketide synthase dehydratase / : / Prismane-like superfamily / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Thiol Ester Dehydrase; Chain A / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Polyketide synthase PksL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.874 Å
AuthorsTill, M. / Ackrill, T.D. / Pernstich, C. / Willis, C.L. / Race, P.R.
CitationJournal: To Be Published
Title: Crystal structure of a monomeric dehydratase domain from a trans AT polyketide synthase split module
Authors: Till, M. / Ackrill, T.D. / Pernstich, C. / Willis, C.L. / Race, P.R.
History
DepositionSep 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polyketide synthase PksL
A: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)62,3472
Polymers62,3472
Non-polymers00
Water2,018112
1
B: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)31,1741
Polymers31,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)31,1741
Polymers31,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.030, 63.820, 66.990
Angle α, β, γ (deg.)89.990, 89.820, 79.230
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 7 - 278 / Label seq-ID: 2 - 273

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

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Components

#1: Protein Polyketide synthase PksL / PKS


Mass: 31173.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: pksL, outG, pksA, pksX, BSU17190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05470
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium/potassium phosphate, 0.1 M Bis-Tris propane, 20% PEG 3350
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.87→66.98 Å / Num. all: 48286 / Num. obs: 48286 / % possible obs: 95 % / Redundancy: 3.8 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Rsym value: 0.058 / Net I/av σ(I): 7.612 / Net I/σ(I): 13.9 / Num. measured all: 184322
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.87-1.983.80.2532.92598467580.1480.2535.191
1.98-2.13.90.1674.52591367130.0980.1677.495.7
2.1-2.243.90.116.72458563690.0650.1110.196
2.24-2.423.80.0878.32261158850.0510.08712.396.2
2.42-2.653.80.06910.22095854660.040.06914.496.2
2.65-2.963.80.05611.41865849120.0330.05617.696.1
2.96-3.423.80.048121620443050.0290.04821.495.5
3.42-4.193.70.04212.91346436080.0250.04224.394.5
4.19-5.933.70.04411.7985426820.0270.04424.991.8
5.93-37.373.80.0412.7609115880.0240.0424.898.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG8

3kg8


Resolution: 1.874→37.39 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2614 / WRfactor Rwork: 0.2369 / FOM work R set: 0.837 / SU B: 3.281 / SU ML: 0.101 / SU R Cruickshank DPI: 0.1689 / SU Rfree: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 2481 5.1 %RANDOM
Rwork0.2244 ---
obs0.2256 46387 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.92 Å2 / Biso mean: 27.234 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0.26 Å20.31 Å2
2--0.23 Å20.05 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.874→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 0 112 4382
Biso mean---23.94 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194345
X-RAY DIFFRACTIONr_bond_other_d0.0030.024175
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9665868
X-RAY DIFFRACTIONr_angle_other_deg1.03439581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4324.639194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8315774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3251520
X-RAY DIFFRACTIONr_chiral_restr0.140.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02992
Refine LS restraints NCS

Ens-ID: 1 / Number: 16873 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.874→1.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 156 -
Rwork0.274 3128 -
all-3284 -
obs--87.6 %

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