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- PDB-2fad: Crystal structure of E. coli heptanoyl-ACP -

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Basic information

Entry
Database: PDB / ID: 2fad
TitleCrystal structure of E. coli heptanoyl-ACP
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / 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 / cytoplasm / cytosol
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
Chem-PM5 / Acyl carrier protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRoujeinikova, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Studies of Fatty Acyl-(Acyl Carrier Protein) Thioesters Reveal a Hydrophobic Binding Cavity that Can Expand to Fit Longer Substrates.
Authors: Roujeinikova, A. / Simon, W.J. / Gilroy, J. / Rice, D.W. / Rafferty, J.B. / Slabas, A.R.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,48413
Polymers17,0292
Non-polymers1,45511
Water3,441191
1
A: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,45010
Polymers8,5141
Non-polymers9359
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0343
Polymers8,5141
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Acyl carrier protein
B: Acyl carrier protein
hetero molecules

A: Acyl carrier protein
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,96826
Polymers34,0574
Non-polymers2,91122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7520 Å2
ΔGint-349 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.257, 106.244, 28.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-407-

ZN

21A-433-

HOH

31A-434-

HOH

41B-439-

HOH

51B-442-

HOH

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Components

#1: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#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.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PM5 / S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) HEPTANETHIOATE


Mass: 454.518 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H35N2O7PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 16351 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.3
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1477 / % possible all: 74

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1L0I

1l0i


Resolution: 1.6→10 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 773 3.8 %5% omitted at random
Rwork0.209 ---
obs-15929 78.8 %-
Solvent computationBsol: 60.276 Å2
Displacement parametersBiso mean: 21.289 Å2
Baniso -1Baniso -2Baniso -3
1--5.574 Å20 Å20 Å2
2--1.663 Å20 Å2
3---3.911 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 67 191 1452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.01
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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