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- PDB-1f7t: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A -

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Basic information

Entry
Database: PDB / ID: 1f7t
TitleHOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A
ComponentsHOLO-(ACYL CARRIER PROTEIN) SYNTHASE
KeywordsTRANSFERASE / 9-strand pseudo beta barrel / LIPID SYNTHESIS
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsParris, K.D. / Lin, L. / Tam, A. / Mathew, R. / Hixon, J. / Stahl, M. / Fritz, C.C. / Seehra, J. / Somers, W.S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.
Authors: Parris, K.D. / Lin, L. / Tam, A. / Mathew, R. / Hixon, J. / Stahl, M. / Fritz, C.C. / Seehra, J. / Somers, W.S.
History
DepositionJun 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96340
Polymers82,1506
Non-polymers1,81334
Water8,449469
1
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98122
Polymers41,0753
Non-polymers90619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-191 kcal/mol
Surface area16070 Å2
MethodPISA
2
D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98218
Polymers41,0753
Non-polymers90715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-168 kcal/mol
Surface area16080 Å2
MethodPISA
3
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules

D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96340
Polymers82,1506
Non-polymers1,81334
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area16460 Å2
ΔGint-368 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.262, 76.160, 85.693
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. The asymmetric unit in this structure contains two such trimers, one constructed from chains A, B, and C. The second from chains D, E. F.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
HOLO-(ACYL CARRIER PROTEIN) SYNTHASE


Mass: 13691.680 Da / Num. of mol.: 6 / Mutation: Q96P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD-HIS / Production host: Escherichia coli (E. coli)
References: UniProt: P96618, holo-[acyl-carrier-protein] synthase

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Non-polymers , 5 types, 503 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 10mM Sodium Acetate pH 4.4, 2mM Magnesium chloride, 100mM sodium chloride, 5mM Dithiothreitol Well: 2.5M Sodium chloride, 0.1M Tris pH 7.0, 0.2M Magnesium chloride, VAPOR DIFFUSION, ...Details: Protein: 10mM Sodium Acetate pH 4.4, 2mM Magnesium chloride, 100mM sodium chloride, 5mM Dithiothreitol Well: 2.5M Sodium chloride, 0.1M Tris pH 7.0, 0.2M Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 M11NaCl
20.1 MTris11
30.2 M11MgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211.2
SYNCHROTRONNSLS X12C20.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 30, 1999
BRANDEIS2CCDJul 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
20.9781
ReflectionResolution: 1.8→20 Å / Num. all: 87902 / Num. obs: 314385 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.76 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.461 / Num. unique all: 3103 / % possible all: 68.6
Reflection
*PLUS
Num. obs: 87902 / Num. measured all: 314385
Reflection shell
*PLUS
% possible obs: 68.6 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4301 5 %Random
Rwork0.196 ---
all0.197 90806 --
obs0.197 85222 93.9 %-
Solvent computationSolvent model: CNS / Bsol: 57.718 Å2 / ksol: 0.393 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 79 469 6141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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