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- PDB-6obv: Structural insights into dehydratase substrate selection for the ... -

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Basic information

Entry
Database: PDB / ID: 6obv
TitleStructural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
Componentsfluvirucin B1 DH domain from module 1
KeywordsLYASE / Polyketide / Dehydratase / Borrelidin / Fluvirucin
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 / oxidoreductase activity / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase dehydratase / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...Polyketide synthase dehydratase / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / 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 / Thiol Ester Dehydrase; Chain A / 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / PAS repeat profile. / PAS domain / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesActinomadura vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMcAndrew, R.P. / Barajas, J.F. / Pereira, J.H. / Keasling, J.D. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: J Ind Microbiol Biotechnol. / Year: 2019
Title: Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.
Authors: Barajas, J.F. / McAndrew, R.P. / Thompson, M.G. / Backman, T.W.H. / Pang, B. / de Rond, T. / Pereira, J.H. / Benites, V.T. / Martin, H.G. / Baidoo, E.E.K. / Hillson, N.J. / Adams, P.D. / Keasling, J.D.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 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: fluvirucin B1 DH domain from module 1
B: fluvirucin B1 DH domain from module 1
C: fluvirucin B1 DH domain from module 1
D: fluvirucin B1 DH domain from module 1


Theoretical massNumber of molelcules
Total (without water)128,3304
Polymers128,3304
Non-polymers00
Water8,935496
1
A: fluvirucin B1 DH domain from module 1
B: fluvirucin B1 DH domain from module 1


Theoretical massNumber of molelcules
Total (without water)64,1652
Polymers64,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area25360 Å2
MethodPISA
2
C: fluvirucin B1 DH domain from module 1
D: fluvirucin B1 DH domain from module 1


Theoretical massNumber of molelcules
Total (without water)64,1652
Polymers64,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-7 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.760, 38.780, 196.970
Angle α, β, γ (deg.)90.000, 103.980, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
fluvirucin B1 DH domain from module 1 / FluA


Mass: 32082.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura vulgaris (bacteria) / Gene: fluA / Production host: Escherichia coli (E. coli) / References: UniProt: J9WMQ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8.5
Details: 0.40 M NaCl, 0.10 M Tris pH 8.5, and 29% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→64.1 Å / Num. obs: 75387 / % possible obs: 89.2 % / Redundancy: 2 % / Biso Wilson estimate: 30.71 Å2 / Net I/σ(I): 12.9
Reflection shellResolution: 2.01→2.04 Å / Num. unique obs: 3800

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
PHENIX1.15rc3_3435refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→19.82 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3259
RfactorNum. reflection% reflection
Rfree0.2632 880 1.3 %
Rwork0.1973 --
obs0.1982 67935 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8214 0 0 496 8710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078401
X-RAY DIFFRACTIONf_angle_d0.90211504
X-RAY DIFFRACTIONf_chiral_restr0.05431309
X-RAY DIFFRACTIONf_plane_restr0.00791551
X-RAY DIFFRACTIONf_dihedral_angle_d5.73144898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.140.36091330.314410649X-RAY DIFFRACTION85.97
2.14-2.30.34021350.273610710X-RAY DIFFRACTION87.05
2.3-2.530.31351300.250810997X-RAY DIFFRACTION88.8
2.53-2.90.29771620.228211127X-RAY DIFFRACTION89.77
2.9-3.650.25471500.183111393X-RAY DIFFRACTION91.15
3.65-19.820.21521700.149412179X-RAY DIFFRACTION94.96
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)
12.79042279696-0.156990534905-0.2317454023292.1498100773-0.4319981963893.91539384588-0.1530259730620.314034228607-0.145678994109-0.05350275550730.188735678485-0.14040225759-0.359466336855-0.119724883554-0.02822474797870.181614025019-0.0296112962310.04538785303870.215708924284-0.01870203806080.14014035952171.17331414987.1244132277869.8586064485
28.6237630194-1.504999622910.7197760188420.987077855729-0.986938769643.8257565603-0.3577700077740.519168163373-1.05537530407-0.3189102829770.507247764607-0.3754418218370.3188771480960.310707568662-0.09071305240760.245713403643-0.03317303999340.05376107025470.29412079436-0.03913197782040.24593177001573.8434342582-0.88514672855562.3099739499
37.17100328978-1.068241545731.757303678271.00155448235-0.2464201145080.600577596866-0.128955520542-0.1654528892270.009950330218-0.04596397983220.169315838645-0.02004524028990.1017236052740.0886750177702-0.01207614573550.17148102811-0.05319623953170.05506099367340.277138069193-0.02594856002050.17793066106662.24562152934.0158174698268.9573829872
44.75573891976-1.37724014153.337334250941.6666345418-1.662201037718.10419447645-0.0826159789429-0.1131945774130.0987189591352-0.143851544554-0.0548698582292-0.227942743799-0.282814271787-0.01462250607350.1182246158950.160911130014-0.002621137551260.06119344550670.120067044041-0.01671079452060.19139495696677.1662607724.64515678238109.89372175
51.685518577180.07261985299810.6238497358421.83461792078-0.1159803004223.68909599790.0350011930716-0.114575841932-0.01310371173050.205822484015-0.0295828949864-0.09823231080850.03772554341810.1209115086060.000593530210040.1246939343720.01199863018180.003031224585360.1249301986-0.0005749388189830.18258627165974.7541060217-0.851703463898124.404872157
65.33393734716-1.66525361486-0.004834011200335.233847195250.4078773405554.64901742343-0.00867000239144-0.255240255476-0.3915342903110.438837009242-0.07715542472330.1594062818570.200640448554-0.1770612543140.1004132069470.1712506311620.01578745689530.01559343860250.157790852745-0.004700633755710.14448542936268.6455040833-1.07426457664130.524138424
77.618495571723.927086022864.263456095125.312089668822.771770631495.79705178639-0.1309475385740.2598171193430.132110963634-0.02616238797950.1898099924160.105089888-0.0457112130912-0.390778789476-0.04036713117070.1750766237990.003930943724340.04481265018670.2780617923110.1333229869730.16421897614854.90667648537.642800893715.97957651862
82.44270357693-0.3950634667920.5287139278333.347078105050.06672606591294.15502586732-0.03111970202670.0257102830395-0.1922358973170.1351868475830.0513628660983-0.09389949451280.03906115123180.04866759245590.06568564749580.1889001462120.01346990706860.01149771800390.1986503104890.04622943081330.13531470492463.09298317532.7437463075415.4642301813
91.623832400040.605082927021-0.3169643679141.839326367120.5383241899765.189992472460.00937166049451-0.302616768620.002745717419870.3067007314970.06435120378880.0552162378892-0.398554628224-0.00823959529687-0.07209204478910.2812833313120.008256438673730.02605979033780.2687457840770.0326792443320.16530516196963.37113353849.087003584134.23881276
105.708031282832.54047487632-0.2067721634311.70064607040.5693308472930.934284525746-0.1019418144770.419993768976-0.348290955810.2202786592970.102096461173-0.2051424641730.082728294096-0.2718691370620.06894443784190.2762791399560.000109362019362-0.02758584036590.3434783876790.1012945967290.18415860393369.39268395472.9758144761629.7373636852
119.478731736560.7524829408954.817241354721.285917577340.3156768887182.45223489901-0.4507400728320.02504918564960.6171284571430.004640542597260.123318216278-0.0686998137339-1.019000479470.002981486628820.4420239332810.392106224065-0.0690637040524-0.04981313934860.1918955046840.03058928570270.28152691747155.973345177412.5885803653-5.97072450847
123.19263225736-0.3487753126060.9928451141443.1875528486-0.4533675740514.825069581970.317386594866-0.209324119394-0.436276871126-0.0674586011287-0.04284768623540.1729994685980.906071519381-0.404260618525-0.1908255522460.423747697973-0.0737666154378-0.1099813325840.2503239452280.050041966560.22965853098152.54338120630.417530682899-14.0767035752
131.76727134635-0.5137868668680.3134103887174.112641532592.039114588875.731159741920.2287662763210.165655792942-0.227380479376-0.1285774149080.0605131554620.1107296433571.34842144171-0.835901850372-0.2371015522490.502721245741-0.110033973729-0.1508078797880.3791890352870.03808722168050.24115322276843.85539110614.51757279474-39.2252253822
144.27098513103-0.4873130150770.2787707747623.408561686040.4059285828633.887807093480.1546006361780.033257952156-0.45597680478-0.512006647570.08451419878140.188897705450.650124313256-0.405593458048-0.07226447593550.363923161921-0.0372687127865-0.08059692557020.2242681374870.01604101145640.20252743257949.34740652924.47467711088-29.5046900943
155.768261391773.07988864416-1.813563769752.10549318418-1.291030776130.8036707781290.113449706741-0.0981282609585-0.916943144754-0.287389065201-0.211863980314-0.1877996305190.580985963820.1799658281620.131898023240.5435633982040.0396781924381-0.1162043779840.332114526169-0.004696665057820.37740511805750.6402568459-3.85892469637-31.3107461383
165.32275166391-2.448277999912.325858791422.72559582997-0.6027371690337.32837124567-0.07813785077610.05496533640840.01074780838120.247962003301-0.102653993665-0.1053267178870.02266066790030.7720853490190.1534372854180.12739650376-0.04189762850320.04401498848040.182620211719-0.03200328306360.16255854874775.54146007036.232106794593.0076086047
172.02130836256-0.5833354517940.6746527148893.20266046154-0.2069059342694.15542615836-0.0022238961841-0.0169766408529-0.1159824991350.211218186610.03179655376740.141548886211-0.0881114020517-0.212519147531-0.008443555295590.10375517764-0.03615721721560.04719429310520.133487691689-0.03322107232040.16848068121567.251828892.9950535883.7880655401
180.3740665850710.2543545098820.376106469243.06577005413-2.625578263316.27347574822-0.09921371187320.333139290289-0.186247636303-0.798758506186-0.186357720129-0.5306237212820.8167198295160.7072117756130.2736661176850.38284555453-0.01881683086580.1435298782450.298900488044-0.01395756871210.38824858380575.1772054866-5.8404382943875.4754101546
192.71075917258-0.00981758233326-0.4624722544382.63207179073-0.7196152529986.046685913470.08839558782380.370499750522-0.154967322912-0.4672189833960.245628744066-0.0679816422752-0.1951380444290.0527506550837-0.1215489925340.286281185672-0.1078240908520.02565140558220.289421946418-0.02571481464210.16056747213270.15148333729.6664333939958.2686311211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 212 through 263 )
2X-RAY DIFFRACTION2chain 'C' and (resid 264 through 282 )
3X-RAY DIFFRACTION3chain 'C' and (resid 283 through 311 )
4X-RAY DIFFRACTION4chain 'D' and (resid 25 through 78 )
5X-RAY DIFFRACTION5chain 'D' and (resid 79 through 253 )
6X-RAY DIFFRACTION6chain 'D' and (resid 254 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 25 through 63 )
8X-RAY DIFFRACTION8chain 'A' and (resid 64 through 162 )
9X-RAY DIFFRACTION9chain 'A' and (resid 163 through 271 )
10X-RAY DIFFRACTION10chain 'A' and (resid 272 through 312 )
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 41 )
12X-RAY DIFFRACTION12chain 'B' and (resid 42 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 211 )
14X-RAY DIFFRACTION14chain 'B' and (resid 212 through 271 )
15X-RAY DIFFRACTION15chain 'B' and (resid 272 through 311 )
16X-RAY DIFFRACTION16chain 'C' and (resid 24 through 63 )
17X-RAY DIFFRACTION17chain 'C' and (resid 64 through 143 )
18X-RAY DIFFRACTION18chain 'C' and (resid 144 through 162 )
19X-RAY DIFFRACTION19chain 'C' and (resid 163 through 211 )

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