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- PDB-6mbh: GphF DH1 P1711L, L1744P variant: An isomerase-inactive variant of... -

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Basic information

Entry
Database: PDB / ID: 6mbh
TitleGphF DH1 P1711L, L1744P variant: An isomerase-inactive variant of GphF DH1
ComponentsGphF Dehydratase 1
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 / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / 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 / Phosphopantetheine attachment site. / Acyl-CoA N-acyltransferase / Thiolase-like / 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
Biological speciesArchangium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Oct 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
A: GphF Dehydratase 1


Theoretical massNumber of molelcules
Total (without water)32,6971
Polymers32,6971
Non-polymers00
Water3,693205
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)34.906, 53.346, 147.084
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 Dehydratase 1


Mass: 32697.045 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 (bacteria) / Strain (production host): BL21 / References: UniProt: U6BSB2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
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 M 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2015
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: 1.7→49.03 Å / Num. obs: 30049 / % possible obs: 95.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.037 / Rrim(I) all: 0.093 / Net I/σ(I): 10.6 / Num. measured all: 177534 / Scaling rejects: 3
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
1.7-1.733.50.948370910530.490.5521.1041.163.5
8.97-49.035.30.05113982660.9970.0240.05724.899.2

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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
Starting model: 3KG9

3kg9


Resolution: 1.7→43.182 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1517 5.07 %
Rwork0.1762 28394 -
obs0.1783 29911 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.98 Å2 / Biso mean: 34.3072 Å2 / Biso min: 14.27 Å2
Refinement stepCycle: final / Resolution: 1.7→43.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 205 2475
Biso mean---40.42 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.75490.33661130.2811935204873
1.7549-1.81760.27241070.24822247235485
1.8176-1.89040.27771310.22832547267897
1.8904-1.97650.27881250.206426732798100
1.9765-2.08070.25021460.180626472793100
2.0807-2.2110.22341430.174326722815100
2.211-2.38170.22941310.177226722803100
2.3817-2.62140.2521530.182126852838100
2.6214-3.00060.22241510.183327052856100
3.0006-3.78010.20081380.163327462884100
3.7801-43.19560.1851790.158328653044100
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)
11.14240.601-0.49952.1813-0.97262.99920.0351-0.13220.1380.2496-0.00770.0409-0.40610.1121-0.02630.2243-0.0052-0.00190.1999-0.02280.21764.20124.7836-12.3989
20.8810.09110.30182.64960.45513.732-0.0444-0.05680.15460.03160.0397-0.0785-0.52140.2650.01090.07-0.01610.00920.21220.00630.20787.7846-0.727-16.054
31.2083-0.26640.34131.8576-0.25592.53220.00480.0208-0.01070.0382-0.0318-0.04260.0090.11880.0220.1316-0.0034-0.00080.16920.010.1716.7051-11.3232-20.7911
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 1985 )A0

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