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- PDB-3o53: Crystal Structure of LRIM1 leucine-rich repeat domain -

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Basic information

Entry
Database: PDB / ID: 3o53
TitleCrystal Structure of LRIM1 leucine-rich repeat domain
ComponentsProtein LRIM1
KeywordsPROTEIN BINDING / leucine-rich repeat
Function / homology
Function and homology information


defense response to symbiont / protein stabilization / extracellular space
Similarity search - Function
: / Dimerization domain in LRIM1 / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBaxter, R.H.G. / Steinert, S. / Chelliah, Y. / Volohonsky, G. / Levashina, E.A. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae.
Authors: Baxter, R.H. / Steinert, S. / Chelliah, Y. / Volohonsky, G. / Levashina, E.A. / Deisenhofer, J.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein LRIM1
B: Protein LRIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2697
Polymers71,2852
Non-polymers9855
Water8,845491
1
A: Protein LRIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1854
Polymers35,6421
Non-polymers5423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein LRIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0853
Polymers35,6421
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Protein LRIM1
hetero molecules

B: Protein LRIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2697
Polymers71,2852
Non-polymers9855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area3350 Å2
ΔGint-17 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.265, 79.265, 238.643
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-481-

HOH

Detailsthe biological unit is a monomer. There are two biological units in the asymmetric unit (chain A and chain B).

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Components

#1: Protein Protein LRIM1 / AGAP006348-PA


Mass: 35642.309 Da / Num. of mol.: 2 / Fragment: residues 23-332, leucine-rich repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: G3 / Gene: AGAP006348, LRIM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7Q5N3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 16% PEG 8000, 0.1M NaCl, 0.1M Na-Hepes, 0.2M Calcium acetate, pH 7.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9794
SYNCHROTRONAPS 19-ID20.97935, 0.97948
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 11, 2008
ADSC Q3152CCDFeb 20, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979351
30.979481
ReflectionResolution: 2→50 Å / Num. obs: 52399 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.067 / Χ2: 1.376 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.034.40.65724790.95195.1
2.03-2.076.10.56525230.96699.1
2.07-2.117.30.54525790.98799.9
2.11-2.157.80.45825921.007100
2.15-2.280.42526051.011100
2.2-2.2580.35125621.056100
2.25-2.3180.27925801.058100
2.31-2.3780.23125931.104100
2.37-2.4480.19926091.109100
2.44-2.5280.17525801.15100
2.52-2.6180.13626321.186100
2.61-2.7180.11625971.251100
2.71-2.847.90.09426401.325100
2.84-2.997.90.07726141.403100
2.99-3.177.90.06826551.494100
3.17-3.427.80.05326411.669100
3.42-3.767.80.04626772.02799.9
3.76-4.317.60.04426652.54599.6
4.31-5.437.40.03727192.14199.5
5.43-507.10.03128571.75196.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.667 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.07 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 2665 5.09 %
Rwork0.1891 --
obs0.1913 52331 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.133 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 290.55 Å2 / Biso mean: 49.7696 Å2 / Biso min: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.5722 Å2-0 Å20 Å2
2---0.5722 Å2-0 Å2
3---1.1444 Å2
Refinement stepCycle: LAST / Resolution: 2→47.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 58 491 5535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410229
X-RAY DIFFRACTIONf_angle_d0.72218441
X-RAY DIFFRACTIONf_chiral_restr0.058809
X-RAY DIFFRACTIONf_plane_restr0.0031603
X-RAY DIFFRACTIONf_dihedral_angle_d15.5122601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9987-2.03510.30891400.26312448258895
2.0351-2.07420.29141380.22492525266399
2.0742-2.11660.28141260.219125822708100
2.1166-2.16260.3011440.215325872731100
2.1626-2.21290.26521270.213625882715100
2.2129-2.26820.26021380.200725862724100
2.2682-2.32960.26191340.203226062740100
2.3296-2.39810.23381600.194425722732100
2.3981-2.47550.251430.185725642707100
2.4755-2.5640.23471390.186126262765100
2.564-2.66660.22741490.179325782727100
2.6666-2.7880.23671430.189126032746100
2.788-2.9350.25411350.188626332768100
2.935-3.11880.24521290.201826362765100
3.1188-3.35960.2361480.192926262774100
3.3596-3.69750.24161420.172926552797100
3.6975-4.23230.17991400.151726862826100
4.2323-5.33110.17541430.141427282871100
5.3311-47.68090.25011470.22542837298498
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)
10.7187-0.80740.59592.29292.0542.92420.1221-0.52510.2502-0.43740.5784-0.20140.2620.1459-0.51630.9238-0.33210.20350.581-0.17610.305-0.304836.229686.4734
20.1764-0.0231-0.48610.13350.28481.80080.2857-0.11360.13990.07360.00310.1583-0.52080.0966-0.26810.5029-0.1040.19040.2195-0.02840.3-6.270428.560674.6325
31.53720.0033-1.12850.57760.03471.14740.04530.15-0.0308-0.0582-0.02040.0398-0.2863-0.0988-0.0520.2891-0.04270.03610.19370.03830.19962.882520.75845.5245
4-0.1809-1.3110.72770.98150.62950.4891-0.10130.2964-0.1510.07310.19790.22340.2411-0.0223-0.02650.2228-0.09490.04370.217-0.04770.216312.10217.148838.3396
50.21520.10460.13230.297-0.59951.21420.1234-0.1428-0.3808-0.33570.45330.42761.0636-1.1242-0.47660.7369-0.7444-0.26430.92630.38750.581-32.508544.448262.705
61.52991.29640.0021.3639-0.26831.1680.0937-0.0849-0.021-0.01640.07450.02490.4839-0.5419-0.13290.3315-0.241-0.04630.29520.08460.2494-19.318453.343462.1173
70.606-0.002-0.83220.40950.05681.87520.0762-0.07390.0412-0.01730.0654-0.08150.21680.1531-0.11890.2434-0.03210.0080.1952-0.0440.27194.864759.06248.9012
80.2534-0.5465-0.16131.45060.16670.12850.1419-0.03170.02910.1754-0.1509-0.056-0.07080.1001-0.0360.2877-0.04040.06420.2884-0.08640.363812.350371.000938.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:45)A24 - 45
2X-RAY DIFFRACTION2(chain A and resid 46:151)A46 - 151
3X-RAY DIFFRACTION3(chain A and resid 152:302)A152 - 302
4X-RAY DIFFRACTION4(chain A and resid 303:339)A303 - 339
5X-RAY DIFFRACTION5(chain B and resid 26:73)B26 - 73
6X-RAY DIFFRACTION6(chain B and resid 74:147)B74 - 147
7X-RAY DIFFRACTION7(chain B and resid 148:302)B148 - 302
8X-RAY DIFFRACTION8(chain B and resid 303:339)B303 - 339

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