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- PDB-3so5: Crystal structure of an Immunoglobulin I-set domain of Lrig3 prot... -

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Basic information

Entry
Database: PDB / ID: 3so5
TitleCrystal structure of an Immunoglobulin I-set domain of Lrig3 protein (Lrig3) from MUS MUSCULUS at 1.70 A resolution
ComponentsLeucine-rich repeats and immunoglobulin-like domains protein 3
KeywordsSIGNALING PROTEIN / Immunoglobulin / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information


otolith morphogenesis / cytoplasmic vesicle membrane / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat ...Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leucine-rich repeats and immunoglobulin-like domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be published
Title: Crystal structure of an Immunoglobulin I-set domain of Lrig3 protein (Lrig3) from MUS MUSCULUS at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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: Leucine-rich repeats and immunoglobulin-like domains protein 3
B: Leucine-rich repeats and immunoglobulin-like domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7828
Polymers25,4482
Non-polymers3346
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-67 kcal/mol
Surface area11230 Å2
MethodPISA
2
A: Leucine-rich repeats and immunoglobulin-like domains protein 3
hetero molecules

B: Leucine-rich repeats and immunoglobulin-like domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7828
Polymers25,4482
Non-polymers3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/41
Buried area2390 Å2
ΔGint-74 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.634, 63.634, 113.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Leucine-rich repeats and immunoglobulin-like domains protein 3 / LIG-3


Mass: 12723.782 Da / Num. of mol.: 2 / Fragment: Immunoglobulin I-set domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BC065142, Kiaa3016, Lrig3 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6P1C6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 490-600 OF THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.5M sodium chloride, 0.2M lithium sulfate, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.9792,0.97892
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
30.978921
ReflectionResolution: 1.7→28.351 Å / Num. all: 26440 / Num. obs: 26440 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.067 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.747.10.6361.21353919040.636100
1.74-1.797.10.5331.51333718660.533100
1.79-1.847.10.4341.81295718130.434100
1.84-1.97.20.3232.41263917620.323100
1.9-1.967.20.243.21231317160.24100
1.96-2.037.20.19441202616740.194100
2.03-2.117.20.15551147515960.155100
2.11-2.197.20.1325.61128015710.132100
2.19-2.297.20.1265.71052714660.126100
2.29-2.47.20.1215.91024814260.121100
2.4-2.537.20.1136.3984313730.113100
2.53-2.697.20.0957.3927712940.095100
2.69-2.877.10.0778.9870912200.077100
2.87-3.17.10.06410.2815011490.064100
3.1-3.47.10.0513.1753410650.05100
3.4-3.870.03817.167669690.038100
3.8-4.396.90.03916.359818630.039100
4.39-5.386.80.03418.350807500.034100
5.38-7.66.50.04115.939256030.041100
7.6-28.3515.70.03617.220463600.03697.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.351 Å / Cor.coef. Fo:Fc: 0.9347 / Cor.coef. Fo:Fc free: 0.9261 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION AND THE PURIFICATION BUFFER RESPECTIVELY HAVE BEEN MODELED INTO THE STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 6.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION AND LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). 7. ELECTON DENSITY INDICATES THAT THE N-TERMINAL GLYCINE RESIDUE (GLY 0) ON SUBUNIT B IS DI-METHYLATED; THEREFORE, THIS RESIDUE WAS MODELED AS DIMETHYL GLYCINE (DMG). 8. DIFFERENCE ELECTRON DENSITY IN A CRYSTAL PACKING INTERFACE NEAR GLU 547 COULD NOT BE RELIABLY ASSIGNED AND WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1337 5.07 %RANDOM
Rwork0.2058 ---
obs0.2063 26373 --
Displacement parametersBiso max: 111.52 Å2 / Biso mean: 35.6376 Å2 / Biso min: 13.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.0379 Å20 Å20 Å2
2--3.0379 Å20 Å2
3----6.0758 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 14 193 1886
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d773SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes273HARMONIC5
X-RAY DIFFRACTIONt_it1789HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion243SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2085SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1789HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2444HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion2
LS refinement shellResolution: 1.7→1.77 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2758 131 4.49 %
Rwork0.2415 2785 -
all0.2431 2916 -
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)
13.03270.0029-0.51621.3401-0.43541.74930.17530.17-0.1455-0.1459-0.11540.00460.23450.0955-0.05990.05170.04170.0053-0.063-0.0103-0.1622-2.39946.878211.0967
23.76051.03661.0261.48130.231.75470.5241-0.1369-0.69250.2133-0.018-0.38890.4952-0.0549-0.50610.0275-0.0325-0.1909-0.17670.0164-0.107321.10482.709615.2322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|496 - 600 }A496 - 600
2X-RAY DIFFRACTION2{ B|0 - 600 }B0 - 600

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