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- PDB-5mh0: Crystal structure of a DM9 domain containing protein from Crassos... -

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Basic information

Entry
Database: PDB / ID: 5mh0
TitleCrystal structure of a DM9 domain containing protein from Crassostrea gigas
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / beta fold
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsWeinert, T. / Warkentin, E. / Pang, G.
CitationJournal: Front Immunol / Year: 2017
Title: DM9 Domain Containing Protein Functions As a Pattern Recognition Receptor with Broad Microbial Recognition Spectrum.
Authors: Jiang, S. / Wang, L. / Huang, M. / Jia, Z. / Weinert, T. / Warkentin, E. / Liu, C. / Song, X. / Zhang, H. / Witt, J. / Qiu, L. / Peng, G. / Song, L.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7213
Polymers15,5371
Non-polymers1842
Water3,315184
1
A: Natterin-3
hetero molecules

A: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4426
Polymers31,0732
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.117, 67.117, 54.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Natterin-3


Mass: 15536.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10011001, CGI_10018577 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K1QRB6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris-HCI, pH 7.0, 20% MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.2→10 Å / Num. all: 45340 / Num. obs: 45250 / % possible obs: 99.8 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.7
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 9590 / Num. unique all: 9516 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.24→9.968 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 12.31
RfactorNum. reflection% reflection
Rfree0.1522 1945 4.93 %
Rwork0.1265 --
obs0.1278 39473 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.24→9.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 12 184 1283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081139
X-RAY DIFFRACTIONf_angle_d0.9021546
X-RAY DIFFRACTIONf_dihedral_angle_d13.847406
X-RAY DIFFRACTIONf_chiral_restr0.088167
X-RAY DIFFRACTIONf_plane_restr0.005199

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