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- PDB-1ebl: THE 1.8 A CRYSTAL STRUCTURE AND ACTIVE SITE ARCHITECTURE OF BETA-... -

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Basic information

Entry
Database: PDB / ID: 1ebl
TitleTHE 1.8 A CRYSTAL STRUCTURE AND ACTIVE SITE ARCHITECTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE III (FABH) FROM ESCHERICHIA COLI
ComponentsBETA-KETOACYL-ACP SYNTHASE III
KeywordsTRANSFERASE / ACYLTRANSFERASE / CONDENSING ENZYME / FATTY ACID SYNTHESIS / LIPID METABOLISM / ALPHA-BETA PROTEIN / FIVE-LAYERED FOLD / COENZYME A BINDING PROTEIN / HELIX DIPOLE / MALONYL COA DECARBOXYLATING ENZYME
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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsDavies, C. / Heath, R.J. / White, S.W. / Rock, C.O.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from escherichia coli.
Authors: Davies, C. / Heath, R.J. / White, S.W. / Rock, C.O.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Isolation and characterization of the beta-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12
Authors: Tsay, J.T. / Oh, W. / Larson, T.J. / Jackowski, S. / Rock, C.O.
History
DepositionJan 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-KETOACYL-ACP SYNTHASE III
B: BETA-KETOACYL-ACP SYNTHASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3814
Polymers67,8462
Non-polymers1,5352
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-29 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.130, 64.300, 165.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.33103, -0.40231, -0.85256), (-0.40502, -0.75642, 0.5136), (-0.85228, 0.51573, 0.08745)
Vector: 1.0E-5, 2.0E-5, 2.0E-5)
DetailsThe biological assembly is a dimer constructed from chain A and chain B as represented in the crystal asymmetric unit.

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Components

#1: Protein BETA-KETOACYL-ACP SYNTHASE III / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / KAS III


Mass: 33923.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8-2.0 M ammonium sulphate, 2% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 50.5 %
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
51.8-2.0 Mammonium sulfate1reservoir
62 %PEG4001reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1
DetectorType: OTHER / Detector: CCD / Date: Jan 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→31.6 Å / Num. all: 230489 / Num. obs: 61752 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.73 % / Biso Wilson estimate: 17.17 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.52
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.88 % / Rmerge(I) obs: 0.14 / Num. unique all: 8193 / % possible all: 89.8
Reflection
*PLUS
Num. measured all: 230489
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Restrained refinement with maximum likelihood residual, Minimization by sparse matrix
RfactorNum. reflection% reflectionSelection details
Rfree0.225 6164 -RANDOM
Rwork0.187 ---
all0.189 230489 --
obs0.189 61640 97.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 96 704 5502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.8
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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