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- PDB-5mh2: Crystal structure of a DM9 domain containing protein from Crassos... -

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Basic information

Entry
Database: PDB / ID: 5mh2
TitleCrystal structure of a DM9 domain containing protein from Crassostrea gigas with D22A mutation
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWeinert, T. / Warkentin, E. / Peng, 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 1.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natterin-3
B: Natterin-3
C: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1347
Polymers61,9714
Non-polymers1633
Water9,368520
1
A: Natterin-3
B: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1134
Polymers30,9852
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area11630 Å2
MethodPISA
2
C: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0213
Polymers30,9852
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-21 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.160, 56.530, 105.530
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Natterin-3


Mass: 15492.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10011001, CGI_10018577 / Production host: Escherichia coli (E. coli) / References: UniProt: K1QRB6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 1.79 Å3/Da / Density % sol: 31.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES, 30% PEG 3350, 0.12M Magnisium Chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 106083 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 17.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.5 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MH0

5mh0


Resolution: 1.3→19.6 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.7
RfactorNum. reflection% reflection
Rfree0.182 5302 5 %
Rwork0.145 --
obs0.147 106069 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 8 520 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184548
X-RAY DIFFRACTIONf_angle_d1.5776184
X-RAY DIFFRACTIONf_dihedral_angle_d14.1511618
X-RAY DIFFRACTIONf_chiral_restr0.139677
X-RAY DIFFRACTIONf_plane_restr0.01793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.31751690.26213207X-RAY DIFFRACTION95
1.3148-1.33020.29891700.26613240X-RAY DIFFRACTION95
1.3302-1.34650.33641740.25823294X-RAY DIFFRACTION98
1.3465-1.36350.33931690.26053221X-RAY DIFFRACTION97
1.3635-1.38140.29061740.23353297X-RAY DIFFRACTION96
1.3814-1.40040.27591720.21233261X-RAY DIFFRACTION98
1.4004-1.42040.24911740.19823308X-RAY DIFFRACTION97
1.4204-1.44160.23931740.1713317X-RAY DIFFRACTION98
1.4416-1.46410.19691740.16543327X-RAY DIFFRACTION99
1.4641-1.48810.22291790.173416X-RAY DIFFRACTION99
1.4881-1.51370.21311750.15973311X-RAY DIFFRACTION100
1.5137-1.54120.22231780.16143392X-RAY DIFFRACTION99
1.5412-1.57090.20281770.14863363X-RAY DIFFRACTION99
1.5709-1.60290.18441770.14323371X-RAY DIFFRACTION100
1.6029-1.63770.18781780.133380X-RAY DIFFRACTION100
1.6377-1.67580.19991790.12713399X-RAY DIFFRACTION100
1.6758-1.71770.17171770.12643362X-RAY DIFFRACTION100
1.7177-1.76410.18221810.1283441X-RAY DIFFRACTION100
1.7641-1.8160.16771760.12443347X-RAY DIFFRACTION100
1.816-1.87460.18331790.1323408X-RAY DIFFRACTION100
1.8746-1.94150.16671790.12913392X-RAY DIFFRACTION100
1.9415-2.01920.16891780.12383388X-RAY DIFFRACTION100
2.0192-2.1110.16631790.12873392X-RAY DIFFRACTION100
2.111-2.22210.15821770.1233378X-RAY DIFFRACTION100
2.2221-2.36110.18261800.13333413X-RAY DIFFRACTION100
2.3611-2.54310.17791790.14443393X-RAY DIFFRACTION100
2.5431-2.79830.17521790.15013416X-RAY DIFFRACTION100
2.7983-3.20170.17711800.14993421X-RAY DIFFRACTION100
3.2017-4.02810.14721810.133428X-RAY DIFFRACTION99
4.0281-19.6020.15861840.13883484X-RAY DIFFRACTION99

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