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- PDB-6x7r: E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) ... -

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Basic information

Entry
Database: PDB / ID: 6x7r
TitleE. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) 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 str. K-12 substr. DH10B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsBenjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-keto-acylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(de-thia)CoA
Authors: Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 15, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _database_2.pdbx_DOI ..._atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_contact_author.id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Oct 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)34,6024
Polymers33,7481
Non-polymers8543
Water7,224401
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)69,2048
Polymers67,4962
Non-polymers1,7086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5220 Å2
ΔGint-28 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.629, 72.629, 102.868
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-796-

HOH

21A-898-

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: 33748.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain: K12 / Gene: fabH, b1091, JW1077 / Variant: DH10B / Plasmid: pRSF / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 39.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 75 mM magnesium chloride, 100 mM HEPES:NaOH, pH 7.5, 23% PEG3350, 1.5% DMSO
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / 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: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 60608 / % possible obs: 99 % / Redundancy: 13.9 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.089 / Rsym value: 0.071 / Χ2: 1.016 / Net I/av σ(I): 25.077 / Net I/σ(I): 130.4
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6013 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.211 / Rrim(I) all: 0.797 / Rsym value: 0.644 / Χ2: 1.034 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.71 Å23.58 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
ARP/wARPmodel building
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HNJ

1hnj


Resolution: 1.35→23.59 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1961 / WRfactor Rwork: 0.1604 / FOM work R set: 0.8552 / SU B: 0.976 / SU ML: 0.039 / SU R Cruickshank DPI: 0.05 / SU Rfree: 0.0543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 3041 5 %RANDOM
Rwork0.1446 ---
obs0.1462 57495 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.29 Å2 / Biso mean: 20.81 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å2-0 Å2
2---1.19 Å20 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 1.35→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 53 413 2821
Biso mean--26.27 33.7 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172391
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.6683478
X-RAY DIFFRACTIONr_angle_other_deg1.5721.5875533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13622.105114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7131516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022861
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02512
LS refinement shellResolution: 1.35→1.383 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.274 232 -
Rwork0.225 4027 -
obs--95.28 %

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