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- PDB-3bdq: Room Tempreture Crystal Structure of Sterol Carrier Protein-2 Like-2 -

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Basic information

Entry
Database: PDB / ID: 3bdq
TitleRoom Tempreture Crystal Structure of Sterol Carrier Protein-2 Like-2
ComponentsSterol carrier protein 2-like 2
KeywordsLIPID TRANSPORT / Alpha/beta protein / lipid carrier / sterol carrier protein
Function / homology
Function and homology information


SCP2 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
Similarity search - Domain/homology
PALMITIC ACID / Sterol carrier protein 2-like 2
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDyer, D.H. / Lan, Q. / Forest, K.T.
CitationJournal: J.Lipid Res. / Year: 2008
Title: Three-dimensional structure/function analysis of SCP-2-like2 reveals differences among SCP-2 family members.
Authors: Dyer, D.H. / Wessely, V. / Forest, K.T. / Lan, Q.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Sterol carrier protein 2-like 2
B: Sterol carrier protein 2-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0165
Polymers23,2472
Non-polymers7693
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.25, 57.25, 49.10
Angle α, β, γ (deg.)90.000, 114.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sterol carrier protein 2-like 2


Mass: 11623.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0GY13
#2: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 microliters AeSCP-2L2 at 10 mg/ml was combined with 2 microliters 1.6 M sodium citrate, 5% glycerol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jul 4, 2006 / Details: Bruker Montel mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 14850 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 4.93 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.033 / Net I/σ(I): 21.24
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.22 % / Mean I/σ(I) obs: 4.97 / Num. unique all: 1977 / Rsym value: 0.194 / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.22 Å41.95 Å
Translation2.22 Å41.95 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.23Adata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.585 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 752 5.1 %RANDOM
Rwork0.186 ---
obs0.188 14836 93.78 %-
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: 21.419 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.09 Å2
2--0.19 Å20 Å2
3----0.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.168 Å0.192 Å
Luzzati sigma a-0.105 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 54 68 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221689
X-RAY DIFFRACTIONr_angle_refined_deg1.1242.0172265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8085216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34626.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68715315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.635158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021160
X-RAY DIFFRACTIONr_nbd_refined0.220.3605
X-RAY DIFFRACTIONr_nbtor_refined0.3180.51150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.59
X-RAY DIFFRACTIONr_mcbond_it1.23721110
X-RAY DIFFRACTIONr_mcangle_it1.87331741
X-RAY DIFFRACTIONr_scbond_it1.322635
X-RAY DIFFRACTIONr_scangle_it2.1733524
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 51 -
Rwork0.193 1021 -
all-1072 -
obs-1021 91.62 %

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