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- PDB-1l0h: CRYSTAL STRUCTURE OF BUTYRYL-ACP FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1l0h
TitleCRYSTAL STRUCTURE OF BUTYRYL-ACP FROM E.COLI
ComponentsACYL CARRIER PROTEIN
KeywordsLIPID TRANSPORT / acyl carrier protein / acyl chain binding / fatty acid biosynthesis
Function / homology
Function and homology information


lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / 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
Acyl carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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_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

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Assembly

Deposited unit
A: ACYL CARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7763
Polymers8,6451
Non-polymers1312
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.360, 63.360, 37.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein ACYL CARRIER PROTEIN / ACP / CAF / CYTOSOLIC ACTIVATING FACTOR


Mass: 8645.460 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 50.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 20000, zinc chloride, 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-IDChemical formulaDetails
16 mg/mlprotein1drop
28-12 %PEG200001reservoir
330 mM1reservoirZnCl2
440 mMsodium cacodylate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 10616 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.269
Reflection
*PLUS
Num. obs: 5485 / % possible obs: 94 % / Num. measured all: 29701 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACP I62M mutant, PDB ENTRY 1L0I

1l0i


Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -5 %RANDOM
Rwork0.205 ---
all-10123 --
obs-10123 --
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms591 0 2 58 651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 9273 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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