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- PDB-3wea: Crystal structure of a Niemann-Pick type C2 protein from Japanese... -

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Basic information

Entry
Database: PDB / ID: 3wea
TitleCrystal structure of a Niemann-Pick type C2 protein from Japanese carpenter ant
ComponentsNiemann-Pick type C2 protein
KeywordsLIPID BINDING PROTEIN / immunoglobulin-like beta-sandwich fold / carrier protein
Function / homology
Function and homology information


sterol binding / sterol transport / extracellular region
Similarity search - Function
Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Niemann-Pick type C2 protein
Similarity search - Component
Biological speciesCamponotus japonicus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFujimoto, Z. / Tsuchiya, W. / Ishida, Y. / Yamazaki, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Niemann-Pick type C2 protein mediating chemical communication in the worker ant
Authors: Ishida, Y. / Tsuchiya, W. / Fujii, T. / Fujimoto, Z. / Miyazawa, M. / Ishibashi, J. / Matsuyama, S. / Ishikawa, Y. / Yamazaki, T.
History
DepositionJul 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Niemann-Pick type C2 protein
B: Niemann-Pick type C2 protein


Theoretical massNumber of molelcules
Total (without water)29,8552
Polymers29,8552
Non-polymers00
Water2,126118
1
A: Niemann-Pick type C2 protein


Theoretical massNumber of molelcules
Total (without water)14,9271
Polymers14,9271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Niemann-Pick type C2 protein


Theoretical massNumber of molelcules
Total (without water)14,9271
Polymers14,9271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.430, 35.652, 104.930
Angle α, β, γ (deg.)90.00, 92.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Niemann-Pick type C2 protein


Mass: 14927.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camponotus japonicus (insect) / Gene: CjapNPC2 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W5JXD9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.2mM sodium chloride, 0.1M HEPES buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→104.843 Å / Num. obs: 28166 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 22.229 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 2747 / Rsym value: 0.495 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HKA

2hka


Resolution: 1.8→22.42 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 4.772 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31671 1400 5 %RANDOM
Rwork0.2589 ---
obs0.26181 26406 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.333 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20.8 Å2
2---1.62 Å20 Å2
3---4.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.168 Å0.169 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 0 118 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9952892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98225.85482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.591154
X-RAY DIFFRACTIONr_chiral_restr0.090.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221552
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 104 -
Rwork0.352 1917 -
obs--97.73 %

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