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- PDB-1f80: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH HOLO-(ACYL C... -

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Basic information

Entry
Database: PDB / ID: 1f80
TitleHOLO-(ACYL CARRIER PROTEIN) SYNTHASE IN COMPLEX WITH HOLO-(ACYL CARRIER PROTEIN)
Components
  • ACYL CARRIER PROTEIN
  • HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
KeywordsTRANSFERASE / 9-strand pseudo beta barrel holo-(acyl carrier protein) acp holo-(acyl carrier protein) synthase acps
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / fatty acid biosynthetic process / magnesium ion binding / membrane / 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 / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...: / 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 / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Acyl carrier protein / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2001Provider: 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: 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 / struct_conn ...database_2 / 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_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ins_code / _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

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: ACYL CARRIER PROTEIN
E: ACYL CARRIER PROTEIN
F: ACYL CARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1487
Polymers68,1256
Non-polymers231
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.458, 122.032, 136.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a trimer of holo-(acyl protein carrier) synthase molecules. This trimer has three active sites and in each of these active sites, a molecule of holo-(acyl carrier protein) is bound.

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Components

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


Mass: 13508.407 Da / Num. of mol.: 3 / Mutation: I2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD / Production host: Escherichia coli (E. coli)
References: UniProt: P96618, holo-[acyl-carrier-protein] synthase
#2: Protein ACYL CARRIER PROTEIN


Mass: 9200.017 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P80643
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: protein: 50mM Bis-Tris pH 6.4, 100mM sodium chloride, 10mM magnesium chloride, 10mM dithiothreitol Well: 0.15-0.3M potassium formate, 15-23% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein11
20.15-0.3 Mpotassium formate12
315-23 %PEG335012
450 mMBis-Tris11pH6.4
5100 mM11NaCl
610 mM11MgCl2
710 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 29694 / Num. obs: 270151 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.56 / Num. unique all: 1396 / % possible all: 94.5
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 29694 / % possible obs: 97.7 % / Num. measured all: 270151
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F7T

1f7t


Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: engh and huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2824 10 %random
Rwork0.222 ---
all0.229 29548 --
obs0.229 28175 95.4 %-
Solvent computationSolvent model: CNS / Bsol: 40.302 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 1 124 4543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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