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- PDB-6mbg: GphF Dehydratase P1711L variant for improved crystallization -

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Basic information

Entry
Database: PDB / ID: 6mbg
TitleGphF Dehydratase P1711L variant for improved crystallization
ComponentsGphF
KeywordsLYASE / dehydratase / polyketide / polyketide synthase / natural product / olefin / isomerase / enoyl-isomerase / epimerase / multifunctional
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...: / Methyltransferase type 12 / Methyltransferase domain / : / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Phosphopantetheine attachment site / Acyl-CoA N-acyltransferase / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Winged helix DNA-binding domain superfamily / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1,4-BUTANEDIOL / GphF
Similarity search - Component
Biological speciesArchangium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 Å
AuthorsDodge, G.J. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)dk042303 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Molecular Basis for Olefin Rearrangement in the Gephyronic Acid Polyketide Synthase.
Authors: Dodge, G.J. / Ronnow, D. / Taylor, R.E. / Smith, J.L.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4235
Polymers32,1281
Non-polymers2954
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.398, 71.658, 78.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GphF


Mass: 32128.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archangium violaceum (bacteria) / Gene: gphF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: U6BSB2
#2: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.12 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1 M trisodium citrate, 20% PEG 4000, 22% 1,4-butanediol, 0.1 mM Hepes pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→44.08 Å / Num. obs: 26083 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 16.1 / Num. measured all: 182544 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.8951.139747514850.6260.5551.2731.494.1
9.07-44.085.70.023155227010.010.02547.899.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.852→44.08 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.93
RfactorNum. reflection% reflection
Rfree0.2104 1996 7.67 %
Rwork0.1775 --
obs0.1801 26022 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.9 Å2 / Biso mean: 36.7953 Å2 / Biso min: 16.63 Å2
Refinement stepCycle: final / Resolution: 1.852→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 19 159 2408
Biso mean--52.41 44.11 -
Num. residues----280
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)
11.9159-0.3836-0.01321.45270.45193.7387-0.0793-0.0091-0.0469-0.0148-0.11360.13130.0654-0.25980.18510.1739-0.0255-0.00220.1747-0.02570.187623.705168.754818.5234
24.2682-0.9128-1.21081.17620.62512.718-0.02860.0564-0.0588-0.0925-0.09040.0932-0.03440.00020.14060.2077-0.0331-0.01010.140.03590.181829.271170.562513.4603
34.54710.498-0.8222.3189-0.07443.045-0.1437-0.1516-0.1448-0.05-0.0587-0.12920.120.05380.17390.16510.02780.01060.1542-0.00150.166440.052667.33499.6206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1700 through 1786 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1787 through 1854 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1855 through 1979 )A0

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