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- PDB-5hst: Crystal structure of the dehydratase domain of MlnB from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5hst
TitleCrystal structure of the dehydratase domain of MlnB from Bacillus amyloliquefaciens
ComponentsPolyketide synthase type I
KeywordsLYASE / polyketide / trans-AT PKS / dehydratase / macrolactin
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / 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 ...Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / 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 / 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
Similarity search - Domain/homology
Polyketide synthase type I
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJakob, R.P. / Dilmi, J. / Hauswirth, 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
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 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 type I
B: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)67,9552
Polymers67,9552
Non-polymers00
Water6,810378
1
B: Polyketide synthase type I

A: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)67,9552
Polymers67,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
A: Polyketide synthase type I

B: Polyketide synthase type I


Theoretical massNumber of molelcules
Total (without water)67,9552
Polymers67,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2710 Å2
ΔGint-16 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.660, 77.440, 138.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Polyketide synthase type I


Mass: 33977.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: pks2B / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1RS66
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, Hepes pH 7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→36.1069 Å / Num. obs: 36974 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.24 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

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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: 2.1→36.102 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 2000 5.41 %
Rwork0.1862 --
obs0.1885 36974 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 0 378 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044293
X-RAY DIFFRACTIONf_angle_d0.6465806
X-RAY DIFFRACTIONf_dihedral_angle_d12.812581
X-RAY DIFFRACTIONf_chiral_restr0.047653
X-RAY DIFFRACTIONf_plane_restr0.004748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.31221410.28872466X-RAY DIFFRACTION100
2.1525-2.21070.30681410.27942457X-RAY DIFFRACTION100
2.2107-2.27570.3161400.25942453X-RAY DIFFRACTION100
2.2757-2.34920.27361410.24092469X-RAY DIFFRACTION100
2.3492-2.43310.28151400.21492445X-RAY DIFFRACTION99
2.4331-2.53050.25561430.20732487X-RAY DIFFRACTION100
2.5305-2.64570.25241390.19792457X-RAY DIFFRACTION100
2.6457-2.78510.22741420.19062483X-RAY DIFFRACTION100
2.7851-2.95950.25281430.18452493X-RAY DIFFRACTION100
2.9595-3.18790.24391440.18882500X-RAY DIFFRACTION100
3.1879-3.50850.2061420.16342504X-RAY DIFFRACTION100
3.5085-4.01560.20571450.15382524X-RAY DIFFRACTION100
4.0156-5.0570.14531460.13452560X-RAY DIFFRACTION100
5.057-36.10690.24151530.19052676X-RAY DIFFRACTION99
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)
12.5205-0.6159-2.15941.39340.41583.1938-0.1341-0.2605-0.00120.17190.0591-0.22270.03040.76170.04480.18350.0184-0.0280.360.00840.224857.16415.25578.7989
22.7636-1.0646-0.08022.48430.28793.0243-0.0021-0.0318-0.02890.1312-0.03730.1021-0.17750.24020.03020.1786-0.03420.0060.1330.00440.149543.182821.166881.5576
33.2945-0.3025-3.30171.25741.01777.1932-0.1274-0.1893-0.1658-0.1092-0.04710.26570.0829-0.2780.14020.1446-0.0236-0.04550.22830.03210.234614.405412.366455.1253
43.56750.7692-0.02413.3236-0.17433.3530.0893-0.3295-0.45220.1731-0.01160.04690.5606-0.39740.0220.2283-0.0684-0.01550.27190.06050.258718.83396.416959.4349
55.37381.1454-3.1672.7388-0.5728.57510.1548-0.51380.5320.1519-0.05670.0802-0.72240.3809-0.03340.2652-0.0569-0.08150.2449-0.07240.335536.45529.240458.3198
63.25871.07670.1972.8243-0.084.3664-0.06160.1332-0.0344-0.20490.0353-0.0106-0.04870.31470.02810.1394-0.0017-0.02520.14940.00630.161632.575818.45546.6944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 292 )
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 71 )
4X-RAY DIFFRACTION4chain 'B' and (resid 72 through 128 )
5X-RAY DIFFRACTION5chain 'B' and (resid 129 through 150 )
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 289 )

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