[English] 日本語
Yorodumi
- PDB-2pet: Lutheran glycoprotein, N-terminal domains 1 and 2. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pet
TitleLutheran glycoprotein, N-terminal domains 1 and 2.
ComponentsLutheran blood group glycoprotein
KeywordsCELL ADHESION / Immunoglobulin superfamily.
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 / MIRAS / Resolution: 1.7 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 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lutheran blood group glycoprotein


Theoretical massNumber of molelcules
Total (without water)25,6481
Polymers25,6481
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.955, 111.062, 35.301
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsAsymmetric unit contains one copy of the biological unit.

-
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.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 12% PEG 20000, 6% heaxane-1,2-diol, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.285 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.285 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
6.8110586000.1180.982.5859393.6
5.9211.8462930.0890.952.5783285.4
8.839.51900180.0980.861.82147189.9
8.9416.11923710.0690.941.82154290.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.810.1081.78.2
4.275.3810010.1021.3558.6
3.734.2710010.1121.1268.5
3.393.7310010.1220.9298.4
3.153.3910010.1410.7397.9
2.963.1598.210.1620.6427.1
2.822.9696.710.1820.5285.8
2.692.8290.410.2240.5634.9
2.592.698110.2290.4543.8
2.52.5970.310.2630.4523
5.385099.420.0641.7887.5
4.275.3810020.0781.3687.7
3.734.2710020.0930.9357.7
3.393.7310020.1130.7487.4
3.153.3999.920.1460.5796.8
2.963.1597.320.1740.4565.5
2.822.9689.220.2040.4094.1
2.692.8275.220.3050.643.1
2.592.6955.920.2840.352.2
2.52.5936.320.3260.3271.8
3.885010030.081.75310.6
3.083.8810030.0861.20610.7
2.693.0810030.0940.85810.7
2.442.6999.930.1170.67410.5
2.272.4499.230.1330.62310
2.132.2798.530.1470.5669.2
2.032.1393.530.1610.5028.2
1.942.0385.330.1840.4696.8
1.861.9470.130.2160.4614.4
1.81.8651.930.2320.4372.8
3.885010040.0561.5910.3
3.083.8810040.0591.34610.4
2.693.0810040.0640.99410.4
2.442.6910040.0810.82810.3
2.272.4499.940.0930.75810.1
2.132.2799.540.1090.6789.8
2.032.1397.440.1250.6218.9
1.942.0387.540.1450.6556.6
1.861.9470.640.1670.594.7
1.81.8649.640.20.5743.3
ReflectionResolution: 1.7→55.64 Å / Num. all: 24823 / Num. obs: 24823 / % possible obs: 89.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.913 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.49 / Num. unique all: 1354 / Χ2: 0.88 / % possible all: 48.3

-
Phasing

PhasingMethod: MIRAS
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 24792
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.56-10053.50.874502
5.19-6.5650.70.892504
4.52-5.1953.20.903510
4.06-4.5252.70.895560
3.71-4.0654.20.877624
3.44-3.7156.50.864693
3.22-3.44570.847723
3.04-3.2257.60.866789
2.89-3.0456.80.844819
2.76-2.8955.70.802854
2.64-2.7656.90.82914
2.54-2.6459.70.816901
2.45-2.5478.40.6431017
2.36-2.4590.60.495971
2.29-2.3691.60.5551057
2.22-2.2987.90.5181056
2.16-2.2288.60.5161110
2.1-2.1688.90.5211131
2.05-2.1900.5551131
2-2.0589.80.5891194
1.96-290.50.5891147
1.91-1.9688.80.5511129
1.87-1.91900.561098
1.84-1.8791.60.5141018
1.8-1.8489.80.511006
1.77-1.891.40.542864
1.73-1.77890.462740
1.7-1.7389.60.438730
Phasing MIRResolution: 1.7→55.64 Å / FOM: 0.735 / Reflection: 8805 / Reflection criterion: FP >3.0 SIGFP
Phasing MIR der

Der set-ID: 1 / Reflection criteria: FPH >3.0 SIGFPH

IDResolution (Å)R cullis acentricR cullis anomalousR cullis centricNum. of sitesPower acentricPower centricReflection acentricReflection anomalousReflection centric
Ptpeak3-500.850.950.9130.960.7148814855197
Ptlr3-500.870.970.9230.920.6848754866196
Auhr2.5-500.510.830.6513.051.7185118509293
Aulr2.5-500.520.880.6712.971.6285108510294
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy anomOccupancy anom suOccupancy isoOccupancy iso su
1Ptpeak88.666Pt0.346-0.0630.0290.7010.0551.1490.079
2Ptpeak39.463Pt0.6610.135-0.0810.40.0320.4970.056
3Ptpeak42.636Pt0.1410.180.3220.580.0340.9280.058
4Ptlr74.646Pt0.346-0.0620.0290.2480.02310.076
5Ptlr25.972Pt0.6610.135-0.0830.1760.0150.4340.053
6Ptlr37.772Pt0.1410.180.3230.2780.0170.8710.058
7Auhr16.176Au0.1520.0260.2980.6270.010.8880.014
8Aulr15.256Au0.1520.0260.2980.2830.0050.8040.014
Phasing MIR shell
Resolution (Å)FOMFOM acentricFOM centricReflectionReflection acentricReflection centric
11.19-55.640.830.820.894978413
6.22-11.190.8160.810.948845533
4.31-6.220.7870.7790.9521158110454
3.29-4.310.7420.7360.9262128206266
2.67-3.290.7140.7080.9193384329193
2.24-2.670.7010.6960.91550151535
1.93-2.24
1.7-1.93

-
Processing

Software
NameVersionClassificationNB
MLPHARECCP4_5.99phasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→55.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.168 / SU B: 4.56 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1229 5 %RANDOM
Rwork0.168 ---
all0.17 24792 --
obs0.17 24792 88.8 %-
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: 21.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.57 Å2
2---1.77 Å20 Å2
3---2.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.113 Å0.112 Å
Refinement stepCycle: LAST / Resolution: 1.7→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 211 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211942
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9652665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09322.60992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91915336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4581523
X-RAY DIFFRACTIONr_chiral_restr0.1210.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021515
X-RAY DIFFRACTIONr_nbd_refined0.2150.2786
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.212
X-RAY DIFFRACTIONr_mcbond_it1.0051.51247
X-RAY DIFFRACTIONr_mcangle_it1.49521971
X-RAY DIFFRACTIONr_scbond_it2.1423780
X-RAY DIFFRACTIONr_scangle_it3.2554.5676
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 (%)
1.699-1.7430.368410.278867206244.035
1.743-1.790.268600.2421121198459.526
1.79-1.8420.305790.2161357196573.079
1.842-1.8990.223700.1971451185881.862
1.899-1.9610.21700.1811619188589.602
1.961-2.030.248720.1671630175896.815
2.03-2.1060.239880.1711587171497.725
2.106-2.1920.2750.1631610169299.586
2.192-2.2890.199850.1711460154799.871
2.289-2.4010.22760.1711433151199.868
2.401-2.5310.191760.18114091485100
2.531-2.6840.217690.17612731342100
2.684-2.8690.225600.16511941254100
2.869-3.0980.207650.15811451210100
3.098-3.3920.216550.1510501105100
3.392-3.7910.172500.145944994100
3.791-4.3740.185500.142848898100
4.374-5.3490.173400.149699739100
5.349-7.530.261330.194547580100
7.53-55.6410.197150.20931933599.701
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)
120.358215.98160.724139.101517.0110.2054-1.22012.12650.5145-1.83640.5951.0638-0.83530.57530.62510.1277-0.0915-0.0990.2230.00270.0104-30.10424.93316.31
22.16162.66110.86743.53771.54241.2088-0.0344-0.060.23930.0487-0.13620.2364-0.0863-0.15860.17060.026-0.00140.00030.0517-0.02810.0649-19.95135.65727.865
320.914411.09833.64269.58723.38823.85690.1535-0.5382-0.5123-0.1003-0.2679-0.0789-0.1286-0.59560.11450.0034-0.00910.00760.16430.016-0.0398-26.69719.06727.075
432.16160.8358-18.66141.71743.30319.29030.25350.72011.9511-0.69540.95790.5917-0.83770.2521-1.21140.1082-0.11970.06690.13380.02790.1141-8.2825.44920.492
57.0038-1.9773-8.6831.04260.874633.6311-0.1833-0.213-0.58380.0168-0.13480.20330.71350.53170.3182-0.00680.00860.02270.00590.00530.0574-12.06721.24725.831
647.73249.25071.08655.7536-3.874916.7427-0.3386-0.7951-0.7204-0.00840.87610.34790.11-1.6206-0.5375-0.032-0.02550.02010.26610.14170.0116-29.11716.67933.193
71.18733.0174-2.22388.5875-5.82984.19980.0417-0.089-0.52190.564-0.5299-1.0206-0.30730.11560.48820.0445-0.0089-0.04820.0470.04870.1298-13.87121.88336.702
89.95267.13360.28365.8129-0.16243.36470.2184-0.13820.46570.443-0.18770.2023-0.2299-0.2013-0.03060.0524-0.00370.02350.0377-0.01010.0276-20.32128.82234.861
93.26643.72171.90915.91862.81311.79920.07770.105-0.25240.0144-0.0632-0.3291-0.0032-0.0907-0.01450.0171-0.02940.01470.0654-0.01430.0307-16.74727.51125.042
1012.46459.75016.04397.86284.14994.34620.0360.1952-0.10840.03720.2281-0.29450.1160.1792-0.26410.02660.00450.00850.0476-0.01740.0966-7.43743.71328.993
1110.61825.9845-1.15353.3734-0.67861.75580.1618-0.3887-0.17310.0943-0.2538-0.0318-0.04930.19720.0920.02920.02080.0360.0692-0.00190.01216.18262.53830.857
125.82729.2107-4.956414.8025-9.25912.53890.2195-0.4088-0.18980.0646-0.3876-0.22070.56211.33040.1681-0.0117-0.00150.04720.2210.0097-0.021423.33867.28219.491
133.53842.4799-0.35381.9364-0.58470.6071-0.0260.023-0.2543-0.10120.0004-0.08090.00220.0210.02560.03890.00450.02230.0461-0.01250.09665.23953.69727.263
147.408-7.4131-0.64938.6289-1.80955.05220.30980.57480.3472-0.0636-0.10870.19790.0606-0.3548-0.20110.01210.0149-0.03010.04870.04850.0854.00767.46521.116
1524.135316.32410.909814.17061.151312.9513-1.1921.8458-1.4118-2.27671.5166-0.470.29050.6527-0.32460.2942-0.06640.04160.1219-0.1187-0.068814.03559.55112.991
168.573610.6344-4.054213.2441-5.779812.4614-0.59030.1838-0.6435-1.1112-0.1259-0.32451.3021-0.17790.71620.1833-0.01250.0609-0.0282-0.06070.015211.56653.50219.82
173.33344.1396-1.79136.353-2.61751.09-0.0280.0714-0.3732-0.0741-0.0814-0.2323-0.0885-0.00120.10940.0516-0.00140.01820.0465-0.00420.07827.11647.33227.108
182.95081.2241-0.60332.1421-0.60120.50140.00320.10160.2043-0.079-0.00290.1155-0.1023-0.0856-0.00030.07760.00540.00650.03970.01510.022210.99269.51224.595
1911.51542.51752.142612.9538-3.65511.76950.10890.02980.22050.1778-0.0943-0.21680.1842-0.0257-0.0146-0.014-0.01310.01370.0509-0.00190.1023-11.15451.56726.569
2012.31947.97180.51995.43740.66560.53950.0893-0.22890.27170.0201-0.10530.3072-0.12480.0260.01590.03640.00570.02580.04470.0190.031710.9866.61531.34
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 41 - 4
225 - 275 - 27
3328 - 3528 - 35
4436 - 4236 - 42
5543 - 4843 - 48
6649 - 5649 - 56
7757 - 7057 - 70
8871 - 8271 - 82
9983 - 10883 - 108
1010109 - 118109 - 118
1111119 - 130119 - 130
1212131 - 136131 - 136
1313137 - 154137 - 154
1414155 - 163155 - 163
1515164 - 171164 - 171
1616172 - 176172 - 176
1717177 - 192177 - 192
1818193 - 209193 - 209
1919210 - 218210 - 218
2020219 - 231219 - 231

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more