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- PDB-3gzl: Crystal Structure of holo PfACP Disulfide-Linked Dimer -

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Basic information

Entry
Database: PDB / ID: 3gzl
TitleCrystal Structure of holo PfACP Disulfide-Linked Dimer
ComponentsAcyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / disulfide dimer / helix bundle / phosphopantetheine / fatty acid biosynthesis / Lipid synthesis / Transit peptide
Function / homology
Function and homology information


acyl binding / acyl carrier activity / mitochondrion
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
4'-PHOSPHOPANTETHEINE / Acyl carrier protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGallagher, J.R. / Prigge, S.T.
CitationJournal: Proteins / Year: 2010
Title: Plasmodium falciparum acyl carrier protein crystal structures in disulfide-linked and reduced states and their prevalence during blood stage growth.
Authors: Gallagher, J.R. / Prigge, S.T.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / 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_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)9,5492
Polymers9,1901
Non-polymers3581
Water00
1
A: Acyl carrier protein
hetero molecules

A: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0974
Polymers18,3812
Non-polymers7172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area2200 Å2
ΔGint-25 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.675, 48.675, 97.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Acyl carrier protein


Mass: 9190.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: ACP, acpP / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: O77077
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.06M NaMalonate, 2mM BME, 1mM CuCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54168 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 19, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54168 Å / Relative weight: 1
ReflectionResolution: 2.49→43.56 Å / Num. all: 3997 / Num. obs: 3981 / % possible obs: 99.6 % / Redundancy: 5.64 % / Rsym value: 0.0679 / Net I/σ(I): 12.95
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 4.09 % / Mean I/σ(I) obs: 3.14 / Num. unique all: 447 / Rsym value: 0.3336 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.2.0019refinement
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1T8K

1t8k


Resolution: 2.55→43.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.844 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 159 4.3 %RANDOM
Rwork0.24062 ---
obs0.2418 3550 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 22 0 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0052.016895
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.019580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74828.7131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98215137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02471
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2258
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2471
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6792411
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2123656
X-RAY DIFFRACTIONr_scbond_it0.3922273
X-RAY DIFFRACTIONr_scangle_it0.5993239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 9 -
Rwork0.296 256 -
obs--100 %

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