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- PDB-3mu3: Crystal structure of chicken MD-1 complexed with lipid IVa -

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Basic information

Entry
Database: PDB / ID: 3mu3
TitleCrystal structure of chicken MD-1 complexed with lipid IVa
ComponentsProtein MD-1
KeywordsIMMUNE SYSTEM / MD-1 / Ly86 / lipid IVa / 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
Chem-LP4 / Chem-LP5 / Lymphocyte antigen 86
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.2Sep 6, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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)37,2739
Polymers34,1492
Non-polymers3,1247
Water1,71195
1
A: Protein MD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5904
Polymers17,0741
Non-polymers1,5163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6825
Polymers17,0741
Non-polymers1,6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.465, 78.150, 101.236
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-LP4 / 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#3: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 46.19 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 17% PEG 2000, 100mM MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0333 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2008 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 12503 / % possible obs: 98.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1213

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID, 3MTX

3mtx


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 18.698 / SU ML: 0.208 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: GLYCEROL MOLECULES (GOL) FROM CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 612 4.9 %RANDOM
Rwork0.23213 ---
obs0.23388 11843 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.058 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2--3.89 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 204 95 2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222435
X-RAY DIFFRACTIONr_bond_other_d0.0020.021716
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0423288
X-RAY DIFFRACTIONr_angle_other_deg0.9923.0243869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9115276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89724.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32315369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5641512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212516
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02458
X-RAY DIFFRACTIONr_mcbond_it1.5431.51384
X-RAY DIFFRACTIONr_mcbond_other0.5061.5558
X-RAY DIFFRACTIONr_mcangle_it2.47222237
X-RAY DIFFRACTIONr_scbond_it4.08731051
X-RAY DIFFRACTIONr_scangle_it5.754.51051
Refine LS restraints NCS

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

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11815tight positional0.060.05
22199tight positional0.060.05
111005loose positional0.065
11815tight thermal0.30.5
22199tight thermal0.230.5
111005loose thermal0.310
LS refinement shellResolution: 2.4→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 35 -
Rwork0.267 815 -
obs--89.76 %
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)
12.66560.13512.28666.17211.22652.1951-0.0137-0.01790.1002-0.2691-0.11170.4662-0.02550.04070.12540.0550.0508-0.00510.1689-0.05270.1625-14.3166.417-11.568
21.63680.3675-0.09361.18370.02342.80480.02030.0499-0.06040.28790.0426-0.1428-0.06280.032-0.06290.08550.0354-0.00740.10570.00860.1651-4.1490.235-12.99
34.30721.6328-1.38944.01460.63241.37810.0246-0.43160.13840.249-0.0035-0.37450.0830.0484-0.02110.12510.0136-0.08080.2987-0.01490.19691.39.421-1.543
42.0543-2.7127-2.97083.62943.56498.2823-0.5899-0.15070.2170.5780.1737-0.35450.9543-0.48690.41620.3497-0.0039-0.00660.29340.01270.38619.3755.409-16.325
50.203-0.0152-0.97662.8407-1.79676.75480.0053-0.077-0.1205-0.0151-0.249-0.2319-0.02950.53120.24370.02380.0550.01130.25160.08170.38860.9181.551-14.501
65.7553.3853-3.89376.1734-3.4595.06980.215-0.2402-0.05110.4789-0.3437-0.213-0.2398-0.03190.12870.06450.0157-0.06080.1433-0.03540.1084-7.5166.523-3.663
74.0403-1.5722-1.30717.40440.08473.1769-0.03830.1848-0.22970.35770.01170.4485-0.0005-0.11120.02660.0434-0.0350.00340.1005-0.03410.13765.275-6.541-26.626
80.72410.2432-0.09440.2601-0.25183.0923-0.0411-0.04730.0439-0.1522-0.0247-0.13080.15850.16050.06580.1616-0.02310.04860.10710.02190.202715.544-0.467-25.13
96.3563-0.81072.51233.7922.18222.95030.09710.5952-0.2285-0.21180.0462-0.31680.06330.2004-0.14330.1401-0.05730.11440.265-0.00010.236220.74-9.46-36.734
105.67235.8242.09176.6884-0.37999.8712-0.46670.0587-0.2708-0.13490.0723-0.4224-1.2995-0.18570.39440.24860.0168-0.04370.2380.02320.297429.043-5.414-22.081
111.6442-2.45282.06764.5358-2.92376.07540.10270.22270.17010.0547-0.2276-0.32110.27750.45620.12490.0928-0.0501-0.01940.26380.05360.322220.574-1.692-23.729
126.0443-4.24764.35257.7652-5.3525.92590.24880.3783-0.0615-0.4616-0.3207-0.03640.32170.0260.07180.06350.00230.0360.1121-0.05770.09612.095-6.525-34.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 45
2X-RAY DIFFRACTION2A46 - 74
3X-RAY DIFFRACTION3A75 - 100
4X-RAY DIFFRACTION4A101 - 110
5X-RAY DIFFRACTION5A111 - 127
6X-RAY DIFFRACTION6A128 - 160
7X-RAY DIFFRACTION7B21 - 45
8X-RAY DIFFRACTION8B46 - 74
9X-RAY DIFFRACTION9B75 - 100
10X-RAY DIFFRACTION10B101 - 110
11X-RAY DIFFRACTION11B111 - 127
12X-RAY DIFFRACTION12B128 - 158

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