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- PDB-6mfc: GphF GNAT-like decarboxylase -

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Basic information

Entry
Database: PDB / ID: 6mfc
TitleGphF GNAT-like decarboxylase
ComponentsGphF
KeywordsLYASE / decarboxylase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : ...Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Gcn5-related N-acetyltransferase (GNAT) / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Thiolase-like / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / 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
Biological speciesCystobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.589 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)50,0837
Polymers49,3302
Non-polymers7535
Water75742
1
B: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0874
Polymers24,6651
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: GphF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9953
Polymers24,6651
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.334, 145.700, 78.006
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.98 Å3/Da / Density % sol: 69.13 %
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

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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: Oct 10, 2017
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.589→43.962 Å / Num. obs: 24892 / % possible obs: 99.7 % / Redundancy: 13.146 % / Biso Wilson estimate: 76.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.184 / Rrim(I) all: 0.192 / Χ2: 1.185 / Net I/σ(I): 11.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.7513.5932.9980.9638930.4983.11498.3
2.75-2.9313.4771.9551.537430.7462.033100
2.93-3.1712.5131.2172.4434850.9171.27100
3.17-3.4712.6290.4856.3432330.9850.506100
3.47-3.8813.8360.24313.1829250.9950.253100
3.88-4.4713.870.15220.5925930.9970.158100
4.47-5.4612.9370.10127.4222200.9980.106100
5.46-7.6712.350.08929.6217540.9980.09399.9
7.67-43.96212.0680.04746.6210460.9990.04999.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2REE

2ree


Resolution: 2.589→43.962 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.5
RfactorNum. reflection% reflection
Rfree0.2718 1242 5 %
Rwork0.2341 --
obs0.236 24860 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.16 Å2 / Biso mean: 91.205 Å2 / Biso min: 53.65 Å2
Refinement stepCycle: final / Resolution: 2.589→43.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 35 42 3011
Biso mean--112.24 77.21 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5888-2.69250.54631360.50512535267197
2.6925-2.8150.51281370.45925822719100
2.815-2.96340.42991370.395926032740100
2.9634-3.1490.32861410.353226032744100
3.149-3.3920.3871360.317826022738100
3.392-3.73320.30921290.214526342763100
3.7332-4.2730.24011410.193226122753100
4.273-5.38210.18241390.171426712810100
5.3821-43.96850.22971460.193627762922100
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)
17.0443-0.7785-0.67134.4531-2.57893.9940.2730.3327-0.2125-0.3269-0.07850.13580.9240.3539-0.25731.0130.0669-0.13690.4613-0.03260.49920.6688-2.0592-13.2997
23.931-0.5015-0.74985.6917-0.86777.83880.22550.07960.1027-0.55060.02650.491-0.4348-0.2554-0.15830.81290.0578-0.10380.47820.03330.553114.73235.3988-12.583
32.07620.2187-3.5161.821-2.17384.00940.44611.3160.9443-0.73950.31030.63990.4025-0.8731-0.08221.1054-0.0485-0.40510.7511-0.06450.83216.36676.2482-19.8904
43.52112.3085-4.86338.0648-3.07486.96260.1721-0.05410.16330.68980.01080.7186-0.6998-0.5646-0.08421.12270.0106-0.12650.72240.01510.72466.417112.1835-9.8627
58.99163.0363-3.0858.826-6.56548.08890.16440.92360.5757-1.4492-0.1390.406-0.03860.80760.11611.4109-0.0961-0.15160.84510.05060.614425.343325.0639-22.1843
66.4476-1.01083.15537.7695-0.41895.018-0.20790.6410.0121-1.73370.32630.2655-1.1491-0.0438-0.09981.2449-0.0384-0.16080.72660.07530.562514.753218.8578-18.8044
79.9472.84674.0327.22041.09974.1599-0.0884-0.00120.4034-0.6166-0.0782-0.1407-0.96270.19090.2131.1122-0.0877-0.02190.54550.04790.456720.680217.3147-12.4178
83.6643-1.09551.50233.99091.46092.1246-0.0397-0.2868-0.07840.28930.1044-0.08330.28120.3054-0.121.46160.151-0.01820.7471-0.05750.543135.5165-25.5362-8.9776
96.62411.3253-5.13035.8803-1.02288.09510.1354-0.0230.2815-0.2030.0202-0.0746-0.5572-0.0008-0.19241.37230.1631-0.06530.6024-0.02740.492732.2782-22.1041-17.3979
103.2955-4.1231-4.77027.22516.41196.26240.30690.1527-0.0142-0.7915-0.47750.01140.0759-0.03480.16441.18540.0853-0.14430.6344-0.01210.502729.9773-28.9443-27.0679
118.6288-3.96391.3124.6457-0.11910.75580.22410.4552-0.2522-0.0821-0.1372-0.0512-0.1441-0.139-0.15381.57460.14770.0430.695-0.04220.527933.1609-29.966-29.9889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 499 through 537 )B499 - 537
2X-RAY DIFFRACTION2chain 'B' and (resid 538 through 600 )B538 - 600
3X-RAY DIFFRACTION3chain 'B' and (resid 601 through 615 )B601 - 615
4X-RAY DIFFRACTION4chain 'B' and (resid 616 through 626 )B616 - 626
5X-RAY DIFFRACTION5chain 'B' and (resid 627 through 654 )B627 - 654
6X-RAY DIFFRACTION6chain 'B' and (resid 655 through 671 )B655 - 671
7X-RAY DIFFRACTION7chain 'B' and (resid 672 through 693 )B672 - 693
8X-RAY DIFFRACTION8chain 'A' and (resid 499 through 537 )A499 - 537
9X-RAY DIFFRACTION9chain 'A' and (resid 538 through 600 )A538 - 600
10X-RAY DIFFRACTION10chain 'A' and (resid 601 through 646 )A601 - 646
11X-RAY DIFFRACTION11chain 'A' and (resid 647 through 693 )A647 - 693

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