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- PDB-3rp1: Crystal structure of Human LAIR-1 in C2 space group -

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Basic information

Entry
Database: PDB / ID: 3rp1
TitleCrystal structure of Human LAIR-1 in C2 space group
ComponentsLeukocyte-associated immunoglobulin-like receptor 1
KeywordsIMMUNE SYSTEM / structural genomics / collagen receptor / New York Structural Genomics Research Consortium / NYSGRC / PSI-Biology / Ig-like / collagen-binding
Function / homology
Function and homology information


immune response-regulating signaling pathway / tertiary granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Neutrophil degranulation / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte-associated immunoglobulin-like receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSampathkumar, P. / Ramagopal, U.A. / Yan, Q. / Toro, R. / Nathenson, S. / Bonanno, J. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of Human LAIR-1 in C2 space group
Authors: Sampathkumar, P. / Ramagopal, U.A. / Yan, Q. / Toro, R. / Nathenson, S. / Bonanno, J. / Almo, S.C.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte-associated immunoglobulin-like receptor 1
B: Leukocyte-associated immunoglobulin-like receptor 1
C: Leukocyte-associated immunoglobulin-like receptor 1
D: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)46,4474
Polymers46,4474
Non-polymers00
Water59433
1
A: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leukocyte-associated immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.117, 77.261, 64.940
Angle α, β, γ (deg.)90.00, 120.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Leukocyte-associated immunoglobulin-like receptor 1 / LAIR-1 / hLAIR1


Mass: 11611.771 Da / Num. of mol.: 4 / Fragment: Extracellular domain (UNP residues 22-123)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD305, LAIR-1, LAIR1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6GTX8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM calcium choloride, 28% PEG400, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12005 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 59.1 Å2 / Rsym value: 0.112 / Net I/σ(I): 17.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4 / Num. unique all: 1173 / Rsym value: 0.639 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGR

3kgr


Resolution: 2.6→31.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.562 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2927 922 7.7 %RANDOM
Rwork0.2108 ---
obs0.2173 11978 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.98 Å2 / Biso mean: 42.1602 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.09 Å2
2---0.16 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 33 3030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223081
X-RAY DIFFRACTIONr_bond_other_d0.0010.022135
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9754205
X-RAY DIFFRACTIONr_angle_other_deg0.80935176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52322.899138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22315466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2381529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_mcbond_it0.4421.51951
X-RAY DIFFRACTIONr_mcbond_other0.0861.5761
X-RAY DIFFRACTIONr_mcangle_it0.90123171
X-RAY DIFFRACTIONr_scbond_it1.50331130
X-RAY DIFFRACTIONr_scangle_it2.5994.51033
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 59 -
Rwork0.319 796 -
all-855 -
obs--98.28 %
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)
13.97571.79211.3472.61721.46014.4138-0.03250.0812-0.0226-0.3436-0.0132-0.07150.08930.42210.04570.09270.04510.00390.06990.03080.154230.2756-2.52887.2052
22.6532.52210.35847.70341.17243.6009-0.1571-0.0319-0.06230.2797-0.0149-0.00480.2279-0.27280.1720.0639-0.0001-0.00570.15010.00830.07915.4405-8.730224.6636
34.30012.5077-0.44974.2987-0.31084.02570.12680.21020.24630.07740.08510.2904-0.5349-0.4511-0.2120.13940.0863-0.03340.16270.02610.142212.27312.46259.4128
44.7152.007-0.53983.96090.65364.64790.02410.5086-0.05380.0445-0.01450.08740.2347-0.5076-0.00970.12460.0589-0.00720.20610.04060.107616.76796.5936-13.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 121
2X-RAY DIFFRACTION1A124 - 130
3X-RAY DIFFRACTION2B26 - 122
4X-RAY DIFFRACTION2B124 - 135
5X-RAY DIFFRACTION3C25 - 122
6X-RAY DIFFRACTION3C124 - 131
7X-RAY DIFFRACTION4D26 - 122
8X-RAY DIFFRACTION4D124 - 129

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