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- PDB-5il6: Crystal structure of the dehydratase domain of RzxB from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 5il6
TitleCrystal structure of the dehydratase domain of RzxB from Pseudomonas fluorescens
ComponentsPolyketide synthase/nonribosomal peptide synthetase hybrid RzxB
KeywordsHYDROLASE / polyketide / macrolactin / trans-AT / pKS / AT-less / dehydratase / rhizoxin
Function / homology
Function and homology information


nonribosomal peptide biosynthetic process / polyketide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
: / RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / Nitroreductase-like / : / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH ...: / RhiE-like, KS-MAT linker domain / Methyltransferase type 12 / Methyltransferase domain / Nitroreductase-like / : / Polyketide synthase dehydratase N-terminal domain / Amino acid adenylation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, ketoreductase domain / KR domain / : / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Phosphopantetheine attachment site / 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
Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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. / Muller, R. / Herbst, D.A. / Maier, T.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 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: Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB
B: Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB


Theoretical massNumber of molelcules
Total (without water)67,0502
Polymers67,0502
Non-polymers00
Water6,918384
1
A: Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB


Theoretical massNumber of molelcules
Total (without water)33,5251
Polymers33,5251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB


Theoretical massNumber of molelcules
Total (without water)33,5251
Polymers33,5251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.480, 105.080, 68.140
Angle α, β, γ (deg.)90.00, 111.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide synthase/nonribosomal peptide synthetase hybrid RzxB


Mass: 33525.215 Da / Num. of mol.: 2 / Fragment: UNP residues 1231-1540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) (bacteria)
Strain: Pf-5 / ATCC BAA-477 / Gene: rzxB, PFL_2989 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCD8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M BisTris 6.5, 0.2 M NaCl, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→63.217 Å / Num. obs: 50913 / % possible obs: 98.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.4 / % possible all: 97.3

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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: 1.9→63.217 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2264 2439 4.79 %
Rwork0.1998 --
obs0.2011 50913 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→63.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 384 4548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034275
X-RAY DIFFRACTIONf_angle_d0.6585820
X-RAY DIFFRACTIONf_dihedral_angle_d12.0632578
X-RAY DIFFRACTIONf_chiral_restr0.045663
X-RAY DIFFRACTIONf_plane_restr0.003778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93890.31291230.2892817X-RAY DIFFRACTION96
1.9389-1.98110.2791310.26062827X-RAY DIFFRACTION98
1.9811-2.02710.20731550.23952869X-RAY DIFFRACTION99
2.0271-2.07780.29011350.2282872X-RAY DIFFRACTION99
2.0778-2.1340.26951390.22772883X-RAY DIFFRACTION99
2.134-2.19680.2221430.2212897X-RAY DIFFRACTION99
2.1968-2.26770.22791360.21152809X-RAY DIFFRACTION98
2.2677-2.34880.24651490.21122840X-RAY DIFFRACTION97
2.3488-2.44280.24551700.21822813X-RAY DIFFRACTION99
2.4428-2.5540.21931360.21982879X-RAY DIFFRACTION99
2.554-2.68870.2521760.21892833X-RAY DIFFRACTION99
2.6887-2.85710.21811440.21412844X-RAY DIFFRACTION98
2.8571-3.07770.26691300.20962820X-RAY DIFFRACTION96
3.0777-3.38740.2341490.2042877X-RAY DIFFRACTION99
3.3874-3.87750.22131480.17992830X-RAY DIFFRACTION98
3.8775-4.8850.17171340.15262843X-RAY DIFFRACTION97
4.885-63.2520.21781410.19292921X-RAY DIFFRACTION98
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)
12.68570.20450.54531.06910.84872.9533-0.06430.0610.1552-0.0785-0.00940.0371-0.0382-0.14670.01850.1981-0.0217-0.00480.14320.00450.176636.919150.415625.2204
22.4561-0.0318-0.4371.7827-0.38431.31680.0956-0.3450.41910.1596-0.0214-0.1074-0.18980.1454-0.10180.2481-0.04530.02310.2069-0.08730.27241.318662.506940.4906
30.88340.2689-1.24910.69770.27473.185-0.0113-0.1603-0.01690.07370.0076-0.20790.03610.16350.04540.19360.0224-0.02630.2707-0.00810.240444.284646.1865-3.4374
43.50781.5222-0.80512.69450.55893.00860.0031-0.01980.04580.1217-0.02790.06380.0861-0.1772-0.05460.17090.0324-0.01620.24220.00870.144933.797344.117-4.5607
51.3610.7859-0.47972.38211.14791.80220.086-0.0423-0.29920.0899-0.059-0.2480.21460.12730.00950.23830.063-0.01530.25390.0070.323445.000427.181-19.0885
61.992-0.32790.74932.4820.0761.2713-0.02380.1104-0.1632-0.1080.0054-0.15060.03650.0488-0.00320.22330.03540.00080.2314-0.00790.225137.282831.3425-19.6212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4370 through 4504 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4505 through 4644 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4369 through 4411 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4412 through 4494 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4495 through 4562 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4563 through 4646 )

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