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- PDB-8d1u: E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) ... -

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Basic information

Entry
Database: PDB / ID: 8d1u
TitleE. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / Ketoacyl synthase / substrate analog
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase-like
Similarity search - Domain/homology
oxa(dethia)-CoA / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 Å
AuthorsBenjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA.
Authors: Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2022ID: 6X7S
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 15, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5773
Polymers33,7901
Non-polymers7872
Water9,116506
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1546
Polymers67,5802
Non-polymers1,5744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4840 Å2
ΔGint-51 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.662, 72.662, 102.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

21A-841-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III / EcFabH


Mass: 33790.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fabH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-UT7 / oxa(dethia)-CoA / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-[(2-hydroxyethyl)amino]-3-oxopropyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate


Mass: 751.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 75 mM Magnesium Chloride, 20% PEG 6000, 3% PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.302→22.992 Å / Num. obs: 68034 / % possible obs: 99.6 % / Redundancy: 14.2 % / Biso Wilson estimate: 14.742 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rsym value: 0.05 / Net I/σ(I): 113.7
Reflection shellResolution: 1.302→1.35 Å / Redundancy: 12 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 4684 / CC1/2: 0.948 / Rpim(I) all: 0.162 / Rsym value: 0.454 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNJ

1hnj


Resolution: 1.302→22.992 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.667 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1668 3446 5.071 %Random
Rwork0.1427 64511 --
all0.144 ---
obs-67957 99.937 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.619 Å20 Å2-0 Å2
2---0.619 Å2-0 Å2
3---1.237 Å2
Refinement stepCycle: LAST / Resolution: 1.302→22.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 49 506 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172481
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.6913634
X-RAY DIFFRACTIONr_angle_other_deg1.551.6035759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38921.901121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63915425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4491518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02541
X-RAY DIFFRACTIONr_nbd_refined0.2210.2517
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22306
X-RAY DIFFRACTIONr_nbtor_refined0.170.21221
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2950.2337
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.222
X-RAY DIFFRACTIONr_nbd_other0.2220.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3910.265
X-RAY DIFFRACTIONr_mcbond_it1.2481.2531315
X-RAY DIFFRACTIONr_mcbond_other1.2391.2521314
X-RAY DIFFRACTIONr_mcangle_it1.7871.8841653
X-RAY DIFFRACTIONr_mcangle_other1.791.8841654
X-RAY DIFFRACTIONr_scbond_it2.2751.561321
X-RAY DIFFRACTIONr_scbond_other2.2741.561322
X-RAY DIFFRACTIONr_scangle_it3.3112.2571959
X-RAY DIFFRACTIONr_scangle_other3.312.2571960
X-RAY DIFFRACTIONr_lrange_it6.03318.1913068
X-RAY DIFFRACTIONr_lrange_other5.70716.6112897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.302-1.3350.2182480.2064684X-RAY DIFFRACTION99.5961
1.335-1.3720.2062550.1844579X-RAY DIFFRACTION100
1.372-1.4120.1822420.174434X-RAY DIFFRACTION100
1.412-1.4550.1822280.1554357X-RAY DIFFRACTION100
1.455-1.5030.1632100.1474203X-RAY DIFFRACTION100
1.503-1.5560.1692360.1474060X-RAY DIFFRACTION100
1.556-1.6140.1621930.1383971X-RAY DIFFRACTION100
1.614-1.680.172040.1383786X-RAY DIFFRACTION100
1.68-1.7550.1561870.1413635X-RAY DIFFRACTION99.9738
1.755-1.840.1542040.1333496X-RAY DIFFRACTION100
1.84-1.940.1731730.1413336X-RAY DIFFRACTION100
1.94-2.0570.1621550.1373188X-RAY DIFFRACTION100
2.057-2.1990.1521490.1322975X-RAY DIFFRACTION100
2.199-2.3750.161480.132788X-RAY DIFFRACTION100
2.375-2.6010.1541520.1372553X-RAY DIFFRACTION100
2.601-2.9080.1751340.1432354X-RAY DIFFRACTION100
2.908-3.3560.183970.142075X-RAY DIFFRACTION100
3.356-4.1070.1651130.1351781X-RAY DIFFRACTION100
4.107-5.7940.147690.1331424X-RAY DIFFRACTION100
5.794-22.9920.181490.181832X-RAY DIFFRACTION97.5637

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