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- PDB-1mzs: CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND di... -

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Basic information

Entry
Database: PDB / ID: 1mzs
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND dichlorobenzyloxy-indole-carboxylic acid inhibitor
Components3-oxoacyl-[acyl-carrier-protein] synthase III
KeywordsTRANSFERASE / FABH
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
Chem-669 / PHOSPHATE ION / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDaines, R.A. / Pendrak, I. / Sham, K. / Van Aller, G.S. / Konstantinidis, A.K. / Lonsdale, J.T. / Janson, C.A. / Qui, X. / Brandt, M. / Silverman, C. / Head, M.S.
CitationJournal: J.Med.Chem. / Year: 2003
Title: First X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling
Authors: Daines, R.A. / Pendrak, I. / Sham, K. / Van Aller, G.S. / Konstantinidis, A.K. / Lonsdale, J.T. / Janson, C.A. / Qiu, X. / Brandt, M. / Khandekar, S.S. / Silverman, C. / Head, M.S.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,1403
Polymers33,5951
Non-polymers5452
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3-oxoacyl-[acyl-carrier-protein] synthase III
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)68,2816
Polymers67,1902
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6570 Å2
ΔGint-76 kcal/mol
Surface area21560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.340, 72.340, 100.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase III / BETA-KETOACYL-ACP synthase III / KAS III


Mass: 33595.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-669 / 1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID


Mass: 450.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21Cl2NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: unknown / Details: Qiu, X., (1999) J.Biol.Chem., 274, 36465.
Components of the solutions
*PLUS
Conc.: 14 % / Common name: PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 14354 / Num. obs: 14354 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.15 / Num. unique all: 1572 / Rsym value: 0.301 / % possible all: 0.92
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1d9b

1d9b
PDB Unreleased entry


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 696 4.3 %RANDOM
Rwork0.175 ---
obs0.1751 13792 85 %-
all-16176 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 35 177 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01012
X-RAY DIFFRACTIONc_angle_deg1.55047
X-RAY DIFFRACTIONc_mcbond_it0.8751.5
X-RAY DIFFRACTIONc_mcangle_it1.3432
X-RAY DIFFRACTIONc_scbond_it1.5352
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3201 64 5.3 %
Rwork0.2675 1199 -
obs-13792 85.3 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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