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- PDB-3mtx: Crystal structure of chicken MD-1 -

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Basic information

Entry
Database: PDB / ID: 3mtx
TitleCrystal structure of chicken MD-1
ComponentsProtein MD-1
KeywordsIMMUNE SYSTEM / MD-1 / Ly86 / RP105 associated protein
Function / homology
Function and homology information


positive regulation of lipopolysaccharide-mediated signaling pathway / inflammatory response / innate immune response / extracellular region
Similarity search - Function
Lymphocyte antigen 86 / 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
TRIETHYLENE GLYCOL / Chem-PGT / Lymphocyte antigen 86
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsYoon, S.I. / Hong, M. / Han, G.W. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of soluble MD-1 and its interaction with lipid IVa.
Authors: Yoon, S.I. / Hong, M. / Han, G.W. / Wilson, I.A.
History
DepositionMay 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein MD-1
B: Protein MD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8936
Polymers34,1492
Non-polymers1,7444
Water2,630146
1
A: Protein MD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9763
Polymers17,0741
Non-polymers9012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9183
Polymers17,0741
Non-polymers8432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.118, 76.494, 101.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Protein MD-1 / Ly-86 / Lymphocyte antigen 86


Mass: 17074.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LY86, MD-1, MD1 / Plasmid: pAcGP67 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 insect cells / References: UniProt: Q90890
#2: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT ...THE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT KNOWN. PGT REPRESENTS A CLOSE MATCH

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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: 46.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 4000, 100 mM Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 1, 2008 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 21878 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.66 / Num. unique all: 2077 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 12.312 / SU ML: 0.149 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A PEG4000 FRAGMENT (PGE) FROM CRYSTALLIZATION SOLUTION AND A GLYCEROL MOLECULE (GOL) FROM CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25182 1095 5 %RANDOM
Rwork0.22119 ---
obs0.22275 20652 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.95 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 110 146 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222317
X-RAY DIFFRACTIONr_bond_other_d0.0050.021624
X-RAY DIFFRACTIONr_angle_refined_deg1.7232.0083123
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0163786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1124.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.48159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
X-RAY DIFFRACTIONr_mcbond_it0.8861.51387
X-RAY DIFFRACTIONr_mcbond_other0.2251.5562
X-RAY DIFFRACTIONr_mcangle_it1.67922244
X-RAY DIFFRACTIONr_scbond_it2.423930
X-RAY DIFFRACTIONr_scangle_it3.9654.5878
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11802tight positional0.040.05
22109medium positional0.430.5
11944loose positional0.045
11802tight thermal0.120.5
22109medium thermal0.252
11944loose thermal0.1310
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 65 -
Rwork0.29 1444 -
obs--96.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1501-0.381-0.38731.93411.1972.5730.07650.1117-0.06120.0005-0.12440.0079-0.1019-0.2710.04790.0159-0.01710.00440.50870.01550.200712.37833.34621.571
23.3991.7343-0.36443.7946-0.81911.9989-0.09070.2865-0.07460.17520.2543-0.3486-0.79140.2686-0.16360.0718-0.0271-0.00610.4933-0.0230.306630.51932.50225.222
34.0954-0.22511.46212.60530.63483.68250.04830.36280.0677-0.171-0.0544-0.1268-0.3759-0.0620.00610.0597-0.00840.03710.4403-0.0110.19217.6336.87522.2
410.1323-2.3862.04545.1584-0.67463.92370.17470.4116-0.0282-0.1919-0.143-0.0047-0.1359-0.2527-0.03170.0379-0.01810.05360.4491-0.01350.160213.58630.19418.343
53.56130.4822-0.82431.9737-1.21132.21230.1179-0.2331-0.01680.014-0.2050.0345-0.12620.15980.0870.0320.0189-0.00750.5421-0.05390.17827.6932.956-8.62
62.2578-2.4176-0.72694.53991.106911.2282-0.0032-0.47940.1281-0.19070.26230.319-0.83210.0652-0.25910.10170.0226-0.01960.6364-0.02710.28279.46632.215-12.281
73.93641.34090.3451.8489-0.39593.36560.3105-0.41870.15170.2349-0.15070.1172-0.41190.0796-0.15980.10160.03110.01590.4802-0.02230.221122.35836.635-9.303
89.86642.65212.04665.41681.70715.04450.3015-0.49980.03230.1992-0.32710.08430.00570.14210.02560.04640.01980.03110.5248-0.04850.135826.31729.844-5.363
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 93
2X-RAY DIFFRACTION2A94 - 110
3X-RAY DIFFRACTION3A111 - 132
4X-RAY DIFFRACTION4A133 - 158
5X-RAY DIFFRACTION5B19 - 93
6X-RAY DIFFRACTION6B94 - 110
7X-RAY DIFFRACTION7B111 - 132
8X-RAY DIFFRACTION8B133 - 158

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