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- PDB-2pf6: Lutheran glycoprotein, N-terminal domains 1 and 2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2pf6
TitleLutheran glycoprotein, N-terminal domains 1 and 2
ComponentsLutheran blood group glycoprotein
KeywordsCELL ADHESION / Immunoglobulin superfamily. Cell adhesion.
Function / homology
Function and homology information


laminin receptor activity / laminin binding / cell-matrix adhesion / transmembrane signaling receptor activity / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Basal cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBurton, N. / Brady, R.L.
CitationJournal: Blood / Year: 2007
Title: The Laminin 511/521-binding site on the Lutheran blood group glycoprotein is located at the flexible junction of Ig domains 2 and 3.
Authors: Mankelow, T.J. / Burton, N. / Stefansdottir, F.O. / Spring, F.A. / Parsons, S.F. / Pedersen, J.S. / Oliveira, C.L. / Lammie, D. / Wess, T. / Mohandas, N. / Chasis, J.A. / Brady, R.L. / Anstee, D.J.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lutheran blood group glycoprotein
B: Lutheran blood group glycoprotein


Theoretical massNumber of molelcules
Total (without water)51,2962
Polymers51,2962
Non-polymers00
Water91951
1
A: Lutheran blood group glycoprotein


Theoretical massNumber of molelcules
Total (without water)25,6481
Polymers25,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lutheran blood group glycoprotein


Theoretical massNumber of molelcules
Total (without water)25,6481
Polymers25,6481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.248, 52.248, 256.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHEAA8 - 368 - 36
21PROPROPHEPHEBB8 - 368 - 36
32ARGARGGLNGLNAA46 - 5346 - 53
42ARGARGGLNGLNBB46 - 5346 - 53
53LEULEUVALVALAA57 - 11257 - 112
63LEULEUVALVALBB57 - 11257 - 112
74ALAALATRPTRPAA114 - 154114 - 154
84ALAALATRPTRPBB114 - 154114 - 154
95GLYGLYARGARGAA171 - 194171 - 194
105GLYGLYARGARGBB171 - 194171 - 194
116SERSERALAALAAA203 - 208203 - 208
126SERSERALAALABB203 - 208203 - 208
137LEULEUTYRTYRAA220 - 231220 - 231
147LEULEUTYRTYRBB220 - 231220 - 231
DetailsAsymmetic unit conatins two copies of biological unit

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Components

#1: Antibody Lutheran blood group glycoprotein / B-CAM cell surface glycoprotein / Auberger B antigen / F8/G253 antigen / CD239 antigen


Mass: 25647.830 Da / Num. of mol.: 2 / Fragment: N-terminal domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAM, LU, MSK19 / Plasmid: pEE / References: UniProt: P50895
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2006
RadiationMonochromator: ASYMMETRIC CUT Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 19830 / Num. obs: 19830 / % possible obs: 90.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.165 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.2 / Num. unique all: 891 / Χ2: 0.633 / % possible all: 41.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å44.56 Å
Translation2.5 Å44.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PET
Resolution: 2.2→85.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.203 / SU B: 14.231 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1014 5.1 %RANDOM
Rwork0.205 ---
all0.207 19755 --
obs0.207 19755 90.11 %-
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 mean: 43.696 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20.6 Å20 Å2
2--1.2 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.255 Å0.442 Å
Refinement stepCycle: LAST / Resolution: 2.2→85.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 51 3643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213670
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9654986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8015460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58522.558172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55815604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131542
X-RAY DIFFRACTIONr_chiral_restr0.0850.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022834
X-RAY DIFFRACTIONr_nbd_refined0.2190.21327
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.214
X-RAY DIFFRACTIONr_mcbond_it1.2371.52364
X-RAY DIFFRACTIONr_mcangle_it1.56123718
X-RAY DIFFRACTIONr_scbond_it2.58231451
X-RAY DIFFRACTIONr_scangle_it3.8844.51268
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
704MEDIUM POSITIONAL0.360.5
646LOOSE POSITIONAL0.645
704MEDIUM THERMAL3.072
646LOOSE THERMAL3.8310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2510.257260.274599156439.962
2.251-2.3130.456540.278830153657.552
2.313-2.380.34570.2721094153574.984
2.38-2.4530.298610.2661250144190.978
2.453-2.5330.284720.2711286140097
2.533-2.6220.295740.2451324140599.502
2.622-2.7210.349690.2412551324100
2.721-2.8320.306650.2381207127399.921
2.832-2.9580.227740.2111146122299.836
2.958-3.1020.295680.2091123119499.749
3.102-3.2690.271670.20710801147100
3.269-3.4670.261590.1811019107999.907
3.467-3.7060.25410.17695099399.799
3.706-4.0030.263420.183913955100
4.003-4.3840.158390.168843882100
4.384-4.90.158370.154757794100
4.9-5.6540.195440.192687731100
5.654-6.9180.219280.211604632100
6.918-9.7520.256290.225465494100
9.752-85.7490.46480.27230932198.754
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
130.253-4.4082-9.25720.81682.09536.027-0.88090.99750.2198-0.1759-0.099-0.1359-0.85220.68360.97990.0648-0.0353-0.0810.09650.05530.277941.462-4.455334.2832
210.05391.44240.53162.27591.53912.2035-0.15570.41750.0135-0.1950.1220.0185-0.11750.08530.03380.161-0.01450.01930.18880.04080.112629.9545-7.070728.6012
315.2665-1.466-3.51813.38015.877210.2832-0.3264-0.6067-0.8871-0.17240.2893-0.26140.50530.67630.03720.1549-0.0048-0.00390.09370.00140.114840.9086-16.156334.7871
413.629-10.0176-13.544519.336316.229124.1016-0.4912-0.39860.75590.76690.33780.9101-0.1044-1.32980.15350.03250.0914-0.01410.28010.04550.097225.1889-9.524346.1871
51.2572-0.4931.90355.26991.58225.031-0.11780.4615-0.1223-0.1970.2941-0.57340.17180.8479-0.17630.0655-0.0435-0.02850.1544-0.04580.156636.6934-19.645835.0137
613.27840.39446.42270.20561.50311.98780.0765-0.8446-0.14730.1989-0.17090.3094-0.09270.40690.09440.1782-0.0566-0.03820.09930.02160.155523.9251-19.760439.0999
71.53740.5882-0.91271.19-1.87892.9668-0.17750.0716-0.1372-0.09160.08470.12030.0481-0.14860.09280.154-0.0356-0.01230.1207-0.00490.159924.9986-15.05529.4935
86.7799-1.19950.69462.4005-0.92750.70250.0055-0.13940.1178-0.02160.04830.0223-0.1541-0.0428-0.05370.1870.0133-0.0110.2082-0.03920.12633.8263-9.822438.3784
927.0574-6.65899.50132.3061-2.11123.41370.2831-0.03560.4306-0.0141-0.2093-0.01480.0678-0.0224-0.07380.13220.02760.03690.19630.06120.095120.0901-3.259832.6317
1010.3096-1.0366-4.94452.39994.2418.4768-0.09580.22660.1654-0.0185-0.23360.3472-0.0924-0.26780.32940.1259-0.0249-0.02250.1480.01910.1362-16.70749.675231.5958
1110.3012-1.286-2.9663.041-0.54923.9084-0.17090.309-0.13790.3487-0.15420.2677-0.3765-0.14320.3250.1933-0.0169-0.02530.1981-0.01690.1133-10.505210.620834.5383
126.4547-4.32692.79383.3989-1.55261.4151-0.0946-0.0238-0.08750.1323-0.075-0.18740.0180.11770.16960.10910.00280.04120.2020.04780.20513.59145.509730.8013
135.94461.0919-4.0850.22650.091430.13070.16870.2990.37220.0453-0.1256-0.2018-0.81910.6201-0.04310.2094-0.0037-0.03940.0233-0.0010.2048-3.221419.181827.5803
149.35428.3311-0.188217.2873-1.27174.42130.0009-0.7522-0.76521.38940.09030.5975-0.60750.2977-0.09120.3069-0.0691-0.00090.1062-0.0670.1457-5.491720.224140.6465
155.8643-6.616-1.810612.2103-0.4081.92450.2014-0.3853-0.2275-0.5189-0.2013-0.24270.33480.381-0.00020.1423-0.013-0.04270.19640.00480.13511.90472.689139.5748
161.3588-1.7332.46932.4707-3.36674.66880.33340.1171-0.1074-0.1406-0.2780.151-0.19990.5152-0.05540.12740.02150.02780.17220.01450.18371.83992.249235.7579
177.5802-1.15260.851813.0841-3.207113.6088-0.18520.00581.2509-0.44960.07890.1652-0.9844-0.70680.10630.118-0.01780.0190.1337-0.03290.1554-13.777319.353331.5326
1818.6388-11.79432.808312.6353-1.42314.5896-0.06440.5242-0.0806-0.1255-0.05030.7042-0.1736-0.48790.11470.0867-0.02240.01120.2014-0.0190.1944-10.230413.989823.9318
1934.0716-9.13693.29123.0955-0.48140.5673-0.11421.23070.770.0747-0.1994-0.3921-0.19150.27620.31360.08150.00330.03360.21530.1150.12697.31596.083423.8593
2028.1092-1.9095-23.12194.3727-0.585343.2715-0.01321.84090.4469-0.21650.47030.6662-0.4549-2.0975-0.45710.0814-0.0092-0.04980.24610.06560.1229-21.249711.981727.0827
215.551310.3763-2.754983.8402-5.50481.36911.0782-0.93790.45034.3203-2.86264.84030.8462-1.34341.78440.1537-0.30680.2940.2748-0.31890.3347-2.1884-10.38148.3602
2221.53136.24265.025816.28748.486914.3761-0.112-0.85090.1781-0.0625-0.47450.6095-0.13880.09730.58650.2502-0.02140.0080.09850.04140.04488.78587.826415.0113
236.27172.16635.578213.1196.256.47220.7485-0.2677-0.38690.3703-1.21681.83481.3293-0.33670.46830.4202-0.2280.03850.16910.01260.16284.9044-14.782712.3378
2417.000915.6454-5.912614.5307-4.335711.2713-0.0589-0.62360.08660.1585-0.0778-0.2895-0.20230.43670.13670.14380.0862-0.08870.1618-0.09210.156710.7058-7.47363.2008
256.40743.4867-1.92832.0323-0.64251.80680.1422-0.0681-0.0195-0.1197-0.02890.22970.39730.2996-0.11330.1712-0.0301-0.080.1526-0.06030.14612.6277-7.5381.1308
2622.496311.231-12.021416.8664-17.694739.4107-0.8123-0.7124-1.82410.52080.2177-1.40061.8799-0.64970.59470.2170.0636-0.07630.16910.05580.127216.2973-17.248211.5241
2710.1264-1.1054-10.59339.0463-1.622311.94670.2810.2187-0.3191-0.3851-0.46680.2266-0.644-0.35060.18580.1128-0.0885-0.07140.258-0.02570.20420.85720.02716.1397
282.972-1.0938-1.19317.2551-1.77752.7580.3301-0.2694-0.05120.9638-0.2013-0.2055-0.29570.4188-0.12870.1947-0.0431-0.05760.2042-0.03050.092713.6713-1.016311.9741
295.08417.2772-0.955420.65811.93848.10120.2128-0.1582-0.16290.6856-0.45850.49080.6602-0.62760.24580.1362-0.0935-0.06930.1733-0.05720.09164.9482-12.72913.6781
302.04074.91390.58618.89791.95860.2107-0.30070.2582-0.1062-0.80780.40240.0283-0.1640.2134-0.10170.294-0.05150.04590.1713-0.04640.05719.572315.205411.3044
318.62165.4126-1.64673.6591-3.18418.02110.41930.55360.98840.1028-0.9022-0.4677-0.8736-0.4050.48280.1392-0.00710.00280.2117-0.02670.139314.374850.85419.6612
322.78232.8580.45175.2318-1.88383.49150.24870.56810.338-0.2359-1.1832-0.53240.1064-0.00380.93450.1690.04470.04450.28250.01540.12311.082941.34758.3239
333.7514-2.60142.14320.59711.5951.7293-0.02970.0648-0.23790.13340.1135-0.07490.08650.0534-0.08380.304-0.0630.07610.1488-0.02420.07359.115423.375110.2665
345.66320.71762.08367.254-3.094617.77680.0560.2395-0.1127-0.25160.19810.07970.6467-1.115-0.25410.0049-0.0023-0.03010.16430.01980.14341.034238.448712.2774
3514.1588-2.06091.98352.61713.35996.0231-0.5843-0.02530.8451-0.37720.44-0.3003-0.1929-0.27680.14420.1467-0.03420.00040.27860.02890.14112.454842.74944.7716
361.4817-2.4898-0.654415.26991.02470.2896-0.2357-0.004-0.1456-0.42840.02140.00190.34230.18780.21430.23260.04520.06750.16760.02040.065112.579627.0784.8164
3711.6791-3.161410.961420.069113.379924.196-1.8066-1.05241.46210.06860.14860.8751-0.9922-0.7121.6580.18640.0549-0.07770.2048-0.10090.22234.612251.458213.9136
384.33852.68422.00449.0377-0.23482.7769-0.0885-0.36140.2650.2835-0.09360.31340.1939-0.1870.18220.1708-0.04840.01490.1717-0.01480.14686.80937.205618.3983
398.347612.3985.071226.98927.49794.05850.4689-0.4072-0.01580.5135-0.61320.66840.5775-0.64140.14420.1102-0.07380.09730.1326-0.01040.09964.253220.923618.0297
406.8281.5374-4.54988.9125-4.685211.0561-0.17860.37320.64360.28620.3971-1.0676-1.0758-0.2831-0.21850.1925-0.02730.0120.1804-0.03740.214.635948.366216.7862
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 71 - 7
22AA8 - 288 - 28
33AA29 - 3529 - 35
44AA36 - 4236 - 42
55AA43 - 6043 - 60
66AA61 - 6761 - 67
77AA68 - 8768 - 87
88AA88 - 10288 - 102
99AA103 - 119103 - 119
1010AA120 - 132120 - 132
1111AA133 - 143133 - 143
1212AA144 - 155144 - 155
1313AA156 - 164156 - 164
1414AA165 - 171165 - 171
1515AA172 - 183172 - 183
1616AA184 - 190184 - 190
1717AA191 - 198191 - 198
1818AA199 - 208199 - 208
1919AA209 - 225209 - 225
2020AA226 - 231226 - 231
2121BB1 - 81 - 8
2222BB9 - 179 - 17
2323BB18 - 3118 - 31
2424BB32 - 3932 - 39
2525BB40 - 5240 - 52
2626BB53 - 6253 - 62
2727BB63 - 7063 - 70
2828BB71 - 9071 - 90
2929BB91 - 10491 - 104
3030BB105 - 123105 - 123
3131BB124 - 132124 - 132
3232BB133 - 143133 - 143
3333BB144 - 153144 - 153
3434BB154 - 168154 - 168
3535BB169 - 173169 - 173
3636BB174 - 192174 - 192
3737BB193 - 200193 - 200
3838BB201 - 209201 - 209
3939BB210 - 223210 - 223
4040BB224 - 231224 - 231

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