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

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Basic information

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


sterol transport / sterol binding
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
OLEIC ACID / Niemann-Pick type C2 protein
Similarity search - Component
Biological speciesCamponotus japonicus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 ...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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Niemann-Pick type C2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2102
Polymers14,9271
Non-polymers2821
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.849, 103.177, 39.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Niemann-Pick type C2 protein


Mass: 14927.394 Da / Num. of mol.: 1
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: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.04 %
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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011
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: 1.7→31.268 Å / Num. obs: 16234 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 16.308 Å2 / Rsym value: 0.106 / Net I/σ(I): 16.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 1576 / Rsym value: 0.443 / % possible all: 100

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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 3WEA

3wea


Resolution: 1.7→31.268 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.48 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26662 814 5 %RANDOM
Rwork0.21616 ---
obs0.21863 15380 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.128 Å0.125 Å
Refinement stepCycle: LAST / Resolution: 1.7→31.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 20 125 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.142.0081465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28725.85441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05315207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.997152
X-RAY DIFFRACTIONr_chiral_restr0.0750.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022784
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 67 -
Rwork0.257 1058 -
obs--94.62 %

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