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- PDB-5il5: Crystal structure of the dehydratase domain of MlnD from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 5il5
TitleCrystal structure of the dehydratase domain of MlnD from Bacillus amyloliquefaciens
ComponentsMlnD
KeywordsLYASE / polyketide / macrolactin / trans-AT / pKS / AT-less / dehydratase / hydrolase
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 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 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase ...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 / 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 / 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
Similarity search - Domain/homology
SDR family NAD(P)-dependent oxidoreductase
Similarity search - Component
Biological speciesBacillus methylotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsJakob, R.P. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: Crystal Structures of Dehydratase Domains from trans-AT Polyketide Biosynthetic Pathways
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: MlnD
B: MlnD


Theoretical massNumber of molelcules
Total (without water)69,8912
Polymers69,8912
Non-polymers00
Water2,990166
1
A: MlnD

A: MlnD


Theoretical massNumber of molelcules
Total (without water)69,8912
Polymers69,8912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
2
B: MlnD

B: MlnD


Theoretical massNumber of molelcules
Total (without water)69,8912
Polymers69,8912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)76.050, 37.950, 166.460
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1676-

HOH

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Components

#1: Protein MlnD


Mass: 34945.383 Da / Num. of mol.: 2 / Fragment: UNP residues 1231-1540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methylotrophicus (bacteria) / Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: mlnD, RBAM_014360 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7Z473
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.9→83.149 Å / Num. obs: 10580 / % possible obs: 97 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.4 / % possible all: 94.8

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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: 2.91→83.149 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.74
RfactorNum. reflection% reflection
Rfree0.2699 523 5.02 %
Rwork0.2279 --
obs0.2299 10422 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.91→83.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 0 166 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054050
X-RAY DIFFRACTIONf_angle_d0.8475470
X-RAY DIFFRACTIONf_dihedral_angle_d13.1342454
X-RAY DIFFRACTIONf_chiral_restr0.053595
X-RAY DIFFRACTIONf_plane_restr0.006721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9101-3.2030.30131470.28082357X-RAY DIFFRACTION94
3.203-3.66640.29431290.22972406X-RAY DIFFRACTION96
3.6664-4.61930.24191160.2012540X-RAY DIFFRACTION98
4.6193-83.1980.25671310.22742596X-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)
11.0025-0.6706-1.19241.16910.89592.35740.1964-0.0610.0568-0.0325-0.0745-0.0183-0.4437-0.00410.24020.38090.04-0.00690.7611-0.0130.073274.86748.27685.8303
20.9784-0.6731-0.62180.9872-0.20121.1613-0.0068-0.24070.09050.12740.0333-0.35-0.23850.4391-0.08840.4328-0.09090.03490.86180.01570.16970.03669.81819.4196
35.3595-1.0387-1.24691.9351-0.95891.36480.19820.1873-0.4978-0.2285-0.25920.06880.22240.05470.00080.46240.08340.02760.57360.02120.095172.3557-1.063911.3178
46.925-2.0973-1.76441.611-0.13790.90990.23050.1317-0.5178-0.179-0.22460.30660.2629-0.0996-0.04330.45580.0287-0.0260.61880.00560.185360.83681.180715.0899
50.9410.03760.89642.15560.62171.013-0.0957-0.5314-0.06140.1788-0.02620.5683-0.1085-1.1390.36670.7881-0.01440.0641.2139-0.19950.420141.348316.097233.4416
61.5783-0.0778-0.84890.57910.28321.7153-0.036-0.6622-0.13640.3778-0.00470.1158-0.1555-0.46120.28290.5545-0.06930.04030.9328-0.02020.137555.247316.92632.3743
72.5052-0.8735-0.34062.39050.95111.6175-0.13890.1180.02190.10940.032-0.10690.1089-0.33430.3230.3631-0.02640.05140.7050.02940.167257.934910.257722.0469
84.213-0.76230.04632.81241.38322.43430.1612-0.0987-0.0731-0.55450.063-0.04950.77620.0094-0.15140.39320.02220.00070.53260.04660.062651.73344.710424.9717
91.42840.3865-1.19580.45820.35452.49750.02130.40660.0671-0.14380.00890.0422-0.2933-0.34110.00610.0894-0.01240.0007-0.14620.00020.417639.45813.191567.436
101.65530.1764-0.35321.3223-0.18741.4303-0.10240.1773-0.2048-0.1016-0.0237-0.31650.04230.18250.05320.08620.02650.02390.0025-0.02670.418152.52862.657259.3189
113.37130.50770.80132.3612-0.39522.4681-0.03030.04540.0172-0.123-0.08010.0877-0.0341-0.20490.18990.07310.02220.02030.0367-0.00190.310854.93521.648759.7129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1259 through 1278 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1279 through 1338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1339 through 1356 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1357 through 1382 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1383 through 1394 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1395 through 1430 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1431 through 1481 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1482 through 1515 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1258 through 1338 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1339 through 1430 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1431 through 1517 )

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