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- PDB-3bkr: Crystal Structure of Sterol Carrier Protein-2 like-3 (SCP2-L3) fr... -

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Basic information

Entry
Database: PDB / ID: 3bkr
TitleCrystal Structure of Sterol Carrier Protein-2 like-3 (SCP2-L3) from Aedes Aegypti
ComponentsSterol Carrier Protein-2 like-3
KeywordsLIPID BINDING PROTEIN / Sterol Carrier / Mosquito / Fatty Acid / Palmitic acid / cholesterol
Function / homologySCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / PALMITIC ACID / AAEL012704-PA
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsDyer, D.H. / Lan, Q. / Forest, K.T.
CitationJournal: Mol.Cell.Biochem. / Year: 2009
Title: Characterization of the yellow fever mosquito sterol carrier protein-2 like 3 gene and ligand-bound protein structure.
Authors: Dyer, D.H. / Vyazunova, I. / Lorch, J.M. / Forest, K.T. / Lan, Q.
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Sterol Carrier Protein-2 like-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4382
Polymers14,1811
Non-polymers2561
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.0, 63.0, 67.8
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein Sterol Carrier Protein-2 like-3


Mass: 14181.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AaeL_AAEL012704 / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q16LC3
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 microl protein at 10mg/ml was mixed with 2microl mother liquor consisting of 25% Peg 8000, 200mM AmSO4, 200mM AmF, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2006
RadiationMonochromator: Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 30511 / % possible obs: 98.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 23.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2946 / Rsym value: 0.3 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.07 Å
Translation2.5 Å23.07 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Polyalanine model derived from 1PZ4

1pz4


Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.91 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1539 5 %RANDOM
Rwork0.186 ---
obs0.188 30499 98.33 %-
all-32038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.063 Å0.058 Å
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 18 168 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221001
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9821346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29225.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00515195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.924157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02714
X-RAY DIFFRACTIONr_nbd_refined0.220.3445
X-RAY DIFFRACTIONr_nbtor_refined0.3170.5718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.5211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.556
X-RAY DIFFRACTIONr_mcbond_it1.1312610
X-RAY DIFFRACTIONr_mcangle_it1.8053981
X-RAY DIFFRACTIONr_scbond_it1.392419
X-RAY DIFFRACTIONr_scangle_it2.0873365
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 120 -
Rwork0.214 2034 -
all-2154 -
obs-2034 96.81 %

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