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- PDB-1fth: CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE ACYL CARRIER PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1fth
TitleCRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE ACYL CARRIER PROTEIN SYNTHASE (3'5'-ADP COMPLEX)
ComponentsACYL CARRIER PROTEIN SYNTHASE
KeywordsTRANSFERASE / Bacterial fatty acid biosynthesis / Acyl carrier synthase / Coenzyme A / structure-based drug design
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
: / 4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChirgadze, N. / Briggs, S. / McAllister, K. / Fischl, A. / Zhao, G.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of Streptococcus pneumoniae acyl carrier protein synthase: an essential enzyme in bacterial fatty acid biosynthesis.
Authors: Chirgadze, N.Y. / Briggs, S.L. / McAllister, K.A. / Fischl, A.S. / Zhao, G.
History
DepositionSep 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: ACYL CARRIER PROTEIN SYNTHASE
B: ACYL CARRIER PROTEIN SYNTHASE
C: ACYL CARRIER PROTEIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8905
Polymers41,0363
Non-polymers8542
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-30 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.188, 62.273, 51.673
Angle α, β, γ (deg.)90.000, 98.745, 90.000
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein ACYL CARRIER PROTEIN SYNTHASE / E.C.2.7.8.7 / ACPS


Mass: 13678.506 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A2W6, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.24 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: VAPOR DIFFUSION, HANGING DROP, pH 4.5 at 294K
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mM1dropMgCl2
314 mM1dropKCl
420 mMTris-HCl1drop
58-15 %PEG40001reservoir
6200 mMammonium sulfate1reservoir
7100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 29541 / Num. obs: 29541 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.1 / % possible all: 99
Reflection
*PLUS
Num. all: 162841 / % possible obs: 100 % / Num. measured all: 304946
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameClassification
AMoREphasing
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTE

1fte


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1457 4.9 %random
Rwork0.238 ---
all-29540 --
obs-29540 98.9 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 54 214 2982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.109
X-RAY DIFFRACTIONc_dihedral_angle_d21.979
X-RAY DIFFRACTIONc_improper_angle_d0.758
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rwork0.336 837 -
obs--99 %
Software
*PLUS
Name: CNX / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.979
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.758
LS refinement shell
*PLUS
Rfactor Rwork: 0.336

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