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- PDB-2x2b: Crystal structure of malonyl-ACP (acyl carrier protein) from Baci... -

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Basic information

Entry
Database: PDB / ID: 2x2b
TitleCrystal structure of malonyl-ACP (acyl carrier protein) from Bacillus subtilis
ComponentsACYL CARRIER PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / PHOSPHOPANTETHEINE / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / 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-SXM / Acyl carrier protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsBellinzoni, M. / Martinez, M.A. / DeMendoza, D. / Alzari, P.M.
CitationJournal: Biochemistry / Year: 2010
Title: A Novel Role of Malonyl-Acp in Lipid Homeostasis.
Authors: Martinez, M.A. / Zaballa, M.E. / Schaeffer, F. / Bellinzoni, M. / Albanesi, D. / Schujman, G.E. / Vila, A.J. / Alzari, P.M. / De Mendoza, D.
History
DepositionJan 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references / Refinement description
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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)9,4894
Polymers8,6541
Non-polymers8353
Water00
1
A: ACYL CARRIER PROTEIN
hetero molecules

A: ACYL CARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9788
Polymers17,3092
Non-polymers1,6696
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area2030 Å2
ΔGint-90.1 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.944, 96.944, 98.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein ACYL CARRIER PROTEIN / ACP


Mass: 8654.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80643
#2: Chemical ChemComp-SXM / 3-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-3-oxopropanoic acid / THIOMALONIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER


Mass: 444.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N2O10PS
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
Has protein modificationY
Nonpolymer detailsTHIOMALONIC ACID S-{2-[3-(2-HYDROXY-3, 3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER
Sequence detailsFIRST GLY RESIDUE IS A PURIFICATION TAG LEFTOVER

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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: 6.89 Å3/Da / Density % sol: 82.2 % / Description: NONE
Crystal growDetails: 2M (NH4)2SO4, 0.1M CITRATE-PHOSPHATE BUFFER PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2007 / Details: MIRRORS
RadiationMonochromator: SI CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→48.5 Å / Num. obs: 6824 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 23.1 % / Biso Wilson estimate: 69.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.4
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 23.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0106refinement
XDSdata reduction
SCALAdata scaling
SHELX-AUTOSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.69→48.47 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.854 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUAL U VALUES ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23297 327 4.8 %RANDOM
Rwork0.21159 ---
obs0.21261 6489 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 15 0 605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5032.003816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.705575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85827.81332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.838152
X-RAY DIFFRACTIONr_chiral_restr0.1030.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02444
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5311.5376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0932606
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9663228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4294.5210
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 26 -
Rwork0.294 461 -
obs--98.38 %
Refinement TLS params.Method: refined / Origin x: 62.838 Å / Origin y: 1.926 Å / Origin z: 31.09 Å
111213212223313233
T0.0522 Å20.0123 Å2-0.0402 Å2-0.1343 Å20.0221 Å2--0.5185 Å2
L8.2363 °20.6864 °21.5222 °2-4.2166 °20.153 °2--5.8772 °2
S-0.0371 Å °-0.0298 Å °-0.087 Å °0.0226 Å °0.0983 Å °-0.3953 Å °0.0782 Å °0.3698 Å °-0.0612 Å °

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