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- PDB-2bdd: Crystal Structure of Holo-ACP-synthase from Plasmodium yoelii -

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Basic information

Entry
Database: PDB / ID: 2bdd
TitleCrystal Structure of Holo-ACP-synthase from Plasmodium yoelii
ComponentsACP-synthase
KeywordsTRANSFERASE / ACP synthase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase activity / metalloendopeptidase activity / fatty acid biosynthetic process / rRNA processing / endonuclease activity / magnesium ion binding
Similarity search - Function
Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / 4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A ...Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / 4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
4'-phosphopantetheinyl transferase domain-containing protein
Similarity search - Component
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDong, A. / Melone, M. / Zhao, Y. / Lew, J. / Koeieradzki, I. / Alam, Z. / Wasney, G. / Vedadi, M. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Melone, M. / Zhao, Y. / Lew, J. / Koeieradzki, I. / Alam, Z. / Wasney, G. / Vedadi, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACP-synthase


Theoretical massNumber of molelcules
Total (without water)20,6151
Polymers20,6151
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ACP-synthase

A: ACP-synthase

A: ACP-synthase


Theoretical massNumber of molelcules
Total (without water)61,8453
Polymers61,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area4980 Å2
ΔGint-25 kcal/mol
Surface area18550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.771, 86.771, 86.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein ACP-synthase


Mass: 20614.961 Da / Num. of mol.: 1 / Fragment: residues 361-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Species: Plasmodium yoelii / Strain: yoelii / Gene: PY06285 / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus RIL
References: UniProt: Q7RB63, citrate lyase holo-[acyl-carrier protein] synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG8000, 0.2M Mg acetate, 0.1M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 6, 2005 / Details: VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→28.9 Å / Num. all: 10191 / Num. obs: 10191 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 6.9
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2.8 / Num. unique all: 493 / Rsym value: 0.936 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collect(MSC)data collection
HKL-2000data scaling
PHASERV. 1.3.1phasing
Coot0.0.33model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F80

1f80


Resolution: 2.28→28.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.296 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.205 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25146 485 4.8 %RANDOM
Rwork0.20028 ---
all0.2027 9689 --
obs0.2027 9689 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.254 Å2
Refinement stepCycle: LAST / Resolution: 2.28→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 45 1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9751369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25325.47642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.544152
X-RAY DIFFRACTIONr_chiral_restr0.1390.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2419
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5161.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49421002
X-RAY DIFFRACTIONr_scbond_it3.1383437
X-RAY DIFFRACTIONr_scangle_it4.7484.5367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 41 -
Rwork0.225 702 -
obs--100 %

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