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- PDB-1f7l: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH COENZYME A A... -

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Basic information

Entry
Database: PDB / ID: 1f7l
TitleHOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH COENZYME A AT 1.5A
ComponentsHOLO-(ACYL CARRIER PROTEIN) SYNTHASE
KeywordsTRANSFERASE / 9-strand pseudo beta barrel protein / coa complex protein / coenzyme a complex
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
COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 1.5 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: Derived calculations / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 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: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5185
Polymers13,6351
Non-polymers8834
Water1,76598
1
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules

A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules

A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55315
Polymers40,9043
Non-polymers2,64912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8730 Å2
ΔGint-78 kcal/mol
Surface area16410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.820, 55.820, 92.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-132-

CA

DetailsThe Biological assembly is a trimer constructed from chain ACPS and the symmetry operators (-y, x-y, z) and (-x+y, -x, z)

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Components

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


Mass: 13634.627 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.87 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: Protein: 10 mM sodium acetate, 2mM magnesium chloride, 100mM sodium chloride, 5mM Dithiothreitol Well: 20% PEG 3350, 0.2M Calcium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M11CaCl2
220 %PEG335011

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12C11.2
SYNCHROTRONALS 5.0.220.978
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: 1.5→100 Å / Num. all: 17170 / Num. obs: 64434 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.307 / Num. unique all: 834 / % possible all: 98.9
Reflection
*PLUS
Num. obs: 17170 / Num. measured all: 64434
Reflection shell
*PLUS
% possible obs: 98.9 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
SHARPphasing
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD, molecular replacement
Starting model: monomer from PDB 1F7T

1f7t


Resolution: 1.5→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 817 5 %Random
Rwork0.185 ---
all0.189 17169 --
obs0.189 16892 98.3 %-
Solvent computationSolvent model: CNS / Bsol: 54.416 Å2 / ksol: 0.3428 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 51 98 1072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

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