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- PDB-1l0i: Crystal structure of butyryl-ACP I62M mutant -

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Basic information

Entry
Database: PDB / ID: 1l0i
TitleCrystal structure of butyryl-ACP I62M mutant
ComponentsAcyl carrier protein
KeywordsLIPID TRANSPORT / acyl carrier protein / acyl chain binding / fatty acid biosynthesis
Function / homology
Function and homology information


lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / Chem-PSR / Acyl carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsRoujeinikova, A. / Baldock, C. / Simon, W.J. / Gilroy, J. / Baker, P.J. / Stuitje, A.R. / Rice, D.W. / Slabas, A.R. / Rafferty, J.B.
Citation
Journal: Structure / Year: 2002
Title: X-ray Crystallographic Studies on Butyryl-ACP Reveal Flexibility of the Structure around a Putative Acyl Chain Binding Site
Authors: Roujeinikova, A. / Baldock, C. / Simon, W.J. / Gilroy, J. / Baker, P.J. / Stuitje, A.R. / Rice, D.W. / Slabas, A.R. / Rafferty, J.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallisation and preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli
Authors: Roujeinikova, A. / Baldock, C. / Simon, W.J. / Gilroy, J. / Baker, P.J. / Stuitje, A.R. / Rice, D.W. / Rafferty, J.B. / Slabas, A.R.
History
DepositionFeb 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300Only the butryl, beta-mercaptoethylamine and phosphate moieties of the acylated 4' ...Only the butryl, beta-mercaptoethylamine and phosphate moieties of the acylated 4' phosphopantetheine group (PSR) attached to ACP were seen in the electron density. The rest of the 4' phosphopantetheine group was modelled in a stereochemically reasonable manner but omitted from the refinement process (occupancies set to 0.00).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,71011
Polymers8,6631
Non-polymers1,04610
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.347, 41.941, 64.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyl carrier protein / ACP / CAF / Cytosolic activating factor


Mass: 8663.499 Da / Num. of mol.: 1 / Mutation: I62M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8

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Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-PSR / THIOBUTYRIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER


Mass: 428.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29N2O8PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, zinc acetate, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Roujeinikova, A., (2002) Acta Crystallogr., Sect.D, 58, 330.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118-23 %PEG40001reservoir
220 mMzinc acetate1reservoir
350 mMsodium cacodylate1reservoirpH6.0
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorDetector: CCD / Date: May 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.2→15 Å / Num. obs: 21956 / % possible obs: 92 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.391 / % possible all: 86
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 12 Å / % possible obs: 92 % / Num. measured all: 73325
Reflection shell
*PLUS
% possible obs: 86 %

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Processing

Software
NameClassification
Adxvdata processing
DENZOdata reduction
SCALEPACKdata scaling
warpntracemodel building
SHELXL-97refinement
WARPNTRACEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→12 Å / Num. parameters: 7330 / Num. restraintsaints: 8289 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.193 -5 %RANDOM
Rwork0.16 ---
all-21868 --
obs-21868 --
Refinement stepCycle: LAST / Resolution: 1.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms597 0 39 162 798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg2.1
X-RAY DIFFRACTIONo_bond_d0.009
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_deg

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