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- PDB-6mfd: GphF GNAT-like decarboxylase in complex with isobutyryl-CoA -

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Basic information

Entry
Database: PDB / ID: 6mfd
TitleGphF GNAT-like decarboxylase in complex with isobutyryl-CoA
ComponentsGphF
KeywordsLYASE / decarboxylase
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 / Gcn5-related N-acetyltransferase (GNAT) / 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. / Aminopeptidase / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ISOBUTYRYL-COENZYME A / GphF
Similarity search - Component
Biological speciesCystobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.794 Å
AuthorsSkiba, M.A. / Tran, C.L. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008353 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
CitationJournal: Structure / Year: 2020
Title: Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis.
Authors: Skiba, M.A. / Tran, C.L. / Dan, Q. / Sikkema, A.P. / Klaver, Z. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.
History
DepositionSep 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: GphF
A: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2487
Polymers49,3302
Non-polymers1,9185
Water25214
1
B: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5022
Polymers24,6651
Non-polymers8381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7465
Polymers24,6651
Non-polymers1,0814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.427, 145.473, 77.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GphF


Mass: 24664.844 Da / Num. of mol.: 2 / Fragment: GNAT-like decarboxylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cystobacter violaceus (bacteria) / Gene: gphF / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U6BSB2
#2: Chemical ChemComp-CO6 / ISOBUTYRYL-COENZYME A / IB-CO6 / Isobutyryl-CoA


Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S / Comment: antibiotic*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30-35% PEG 3350, 0.23-0.3 M Ammonium Acetate, 0.1 M BisTris HCl pH 5.5, 2.5 mM isobutyryl-CoA

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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 12, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.79→45.614 Å / Num. obs: 19080 / % possible obs: 99.5 % / Redundancy: 6.756 % / Biso Wilson estimate: 67.257 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.19 / Χ2: 1.12 / Net I/σ(I): 9.88 / Num. measured all: 128906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.79-2.966.9591.6951.320612303829620.7371.83197.5
2.96-3.177.0171.0912.1120097286628640.8811.17899.9
3.17-3.426.820.5693.8818243267526750.9540.616100
3.42-3.746.4580.2897.3915978247424740.9870.314100
3.74-4.186.5950.18411.3514845225122510.9930.2100
4.18-4.827.0580.11317.1414166200820070.9970.122100
4.82-5.896.7890.11217.0511521169716970.9970.121100
5.89-8.286.2990.07921.148479134713460.9980.08699.9
8.28-45.6146.1750.03540.6149658158040.9990.03898.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3211refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFC

6mfc


Resolution: 2.794→45.614 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 940 4.94 %
Rwork0.243 18090 -
obs0.245 19030 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.53 Å2 / Biso mean: 108.1898 Å2 / Biso min: 54.85 Å2
Refinement stepCycle: final / Resolution: 2.794→45.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 122 14 3070
Biso mean--137.89 62.6 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7941-2.94140.4311260.40772474260097
2.9414-3.12570.39161340.395725652699100
3.1257-3.36690.40491370.332625522689100
3.3669-3.70560.32471370.267225722709100
3.7056-4.24150.30511210.229525982719100
4.2415-5.34250.23291430.183526102753100
5.3425-45.62010.20941420.196627192861100
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)
12.6815-0.0361-2.298.7457-2.64272.75730.52870.0753-0.2501-0.3666-0.24610.36530.16340.0454-0.35221.92060.0018-0.1240.5696-0.07570.659917.6311-5.0479-16.7545
23.78641.2999-2.28926.83770.73284.86020.02510.2471-0.1182-0.34290.1765-0.0476-0.13430.10690.06721.84220.0848-0.16380.5412-0.06250.694123.76691.5684-9.3734
34.0711-3.0144-3.77417.2146.94336.94880.63870.1759-0.4285-0.3803-0.28350.5561.1818-0.96980.12871.9099-0.0259-0.43470.5982-0.00160.676712.4506-0.5115-14.9246
43.9551-0.1291-0.74725.6881.15423.48890.3928-0.39810.15420.5034-0.06810.5334-0.03160.477-0.06352.0570.16030.00040.4227-0.04620.759814.769311.2184-5.3103
52.30911.70961.15763.69140.7871.87520.46430.49760.3666-0.1657-0.00010.51540.84910.1526-0.28841.72660.0728-0.2280.67220.11560.612514.357510.911-19.7535
63.74761.2467-1.09134.5417-3.45173.39350.16880.80540.3719-0.8934-0.12881.2549-0.10010.454-0.11961.9617-0.0774-0.09370.7850.04370.707522.150327.3806-21.6932
75.06531.55270.94142.79620.46093.4215-0.3168-0.3062-0.2147-1.0488-0.04480.5135-0.19390.05340.2892.00090.0239-0.10420.50850.00140.626717.658317.8725-14.7985
80.40880.26880.56960.16030.37460.95260.2272-0.4192-0.2391-0.16830.06310.31110.2384-0.46220.87042.45250.07190.01890.6152-0.25940.160630.1366-25.5382-6.478
90.44880.03320.17120.09810.00020.1750.04490.27480.3089-0.149-0.25120.1408-0.44660.95670.18792.07750.1271-0.09090.8296-0.07290.516440.2091-25.5688-12.2471
100.76090.28030.07150.6304-0.08322.0736-0.3599-0.18430.03720.3013-0.01590.0160.2084-0.3233-0.04212.10560.0928-0.08740.479-0.13840.675326.1017-21.2919-9.15
111.0585-0.2891-0.45930.23370.83243.5036-0.0111-0.19880.2558-0.2945-0.1748-0.0836-0.322-0.6402-0.23972.26040.18740.00410.6181-0.09840.40431.0401-21.3151-14.4124
122.8244-2.16261.42692.4993-2.24952.4137-0.00670.50920.7262-0.43420.0293-0.8332-0.6720.47030.2332.28030.0482-0.03290.6729-0.10860.493537.6748-18.197-23.669
130.77090.4083-0.44833.69940.23090.8829-0.1324-0.0636-0.07680.22780.14660.81950.7846-0.42170.02622.01010.116-0.07560.7301-0.11830.694321.3656-27.0577-16.7702
140.14640.0756-0.12030.32770.1360.1667-0.02370.0758-0.0315-0.0644-0.08870.0106-0.00250.2591-0.03192.54620.2163-0.01150.5535-0.25850.280931.383-26.0963-26.6625
150.34350.05270.29293.20061.00980.657-0.35370.0505-0.14870.0615-0.0521-0.02790.02610.07810.05222.32740.21990.09210.5432-0.18150.364436.2383-40.3121-35.8761
162.5773-1.79160.29691.6018-0.63730.615-0.11680.8672-0.5902-0.3524-0.09890.26140.0053-0.111-0.46822.02170.19570.03550.69610.03240.501928.2762-31.5367-32.2318
170.11420.16480.12440.88010.72210.59260.2580.3290.1216-0.0723-0.02480.1335-0.81530.27460.06012.2742-0.02660.00470.6881-0.05060.623843.8404-32.4812-26.9224
180.64940.38730.8180.28290.16032.91420.1672-0.0539-0.3643-0.1104-0.337-0.23241.14340.4663-1.55651.50880.2878-0.0466-0.0825-0.4079-0.06627.8693-20.6934-30.3831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 499 through 519 )B499 - 519
2X-RAY DIFFRACTION2chain 'B' and (resid 520 through 537 )B520 - 537
3X-RAY DIFFRACTION3chain 'B' and (resid 538 through 560 )B538 - 560
4X-RAY DIFFRACTION4chain 'B' and (resid 561 through 592 )B561 - 592
5X-RAY DIFFRACTION5chain 'B' and (resid 593 through 636 )B593 - 636
6X-RAY DIFFRACTION6chain 'B' and (resid 637 through 654 )B637 - 654
7X-RAY DIFFRACTION7chain 'B' and (resid 655 through 693 )B655 - 693
8X-RAY DIFFRACTION8chain 'A' and (resid 499 through 519 )A499 - 519
9X-RAY DIFFRACTION9chain 'A' and (resid 520 through 537 )A520 - 537
10X-RAY DIFFRACTION10chain 'A' and (resid 538 through 549 )A538 - 549
11X-RAY DIFFRACTION11chain 'A' and (resid 550 through 560 )A550 - 560
12X-RAY DIFFRACTION12chain 'A' and (resid 561 through 592 )A561 - 592
13X-RAY DIFFRACTION13chain 'A' and (resid 593 through 615 )A593 - 615
14X-RAY DIFFRACTION14chain 'A' and (resid 616 through 633 )A616 - 633
15X-RAY DIFFRACTION15chain 'A' and (resid 634 through 645 )A634 - 645
16X-RAY DIFFRACTION16chain 'A' and (resid 646 through 671 )A646 - 671
17X-RAY DIFFRACTION17chain 'A' and (resid 672 through 684 )A672 - 684
18X-RAY DIFFRACTION18chain 'A' and (resid 685 through 693 )A685 - 693

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