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- PDB-1uz8: anti-Lewis X Fab fragment in complex with Lewis X -

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Basic information

Entry
Database: PDB / ID: 1uz8
Titleanti-Lewis X Fab fragment in complex with Lewis X
Components
  • IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A
  • IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A
KeywordsIMMUNE SYSTEM / ANTIBODY / ANTI-CARBOHYDRATE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVan Roon, A.M.M. / Pannu, N.S. / De Vrind, J.P.M. / Hokke, C.H. / Deelder, A.M. / Van Der marel, G.A. / Van Boom, J.H. / Abrahams, J.P.
CitationJournal: Structure / Year: 2004
Title: Structure of an Anti-Lewis X Fab Fragment in Complex with its Lewis X Antigen
Authors: Van Roon, A.M.M. / Pannu, N.S. / De Vrind, J.P.M. / Van Der Marel, G.A. / Van Boom, J.H. / Hokke, C.H. / Deelder, A.M. / Abrahams, J.P.
History
DepositionMar 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A
B: IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A
H: IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A
L: IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0866
Polymers93,9994
Non-polymers1,0872
Water5,170287
1
A: IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A
B: IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5433
Polymers47,0002
Non-polymers5441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-11.5 kcal/mol
Surface area19870 Å2
MethodPISA
2
H: IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A
L: IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5433
Polymers47,0002
Non-polymers5441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-12 kcal/mol
Surface area20160 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-6.9 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.104, 60.778, 91.556
Angle α, β, γ (deg.)95.98, 95.41, 101.71
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3981, -0.64951, 0.64781), (-0.65656, -0.69492, -0.29327), (0.64066, -0.30858, -0.70309)
Vector: 0.19667, 44.5805, 48.39019)

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Components

#1: Antibody IGG FAB (IGG3, KAPPA) LIGHT CHAIN 291-2G3-A


Mass: 24065.650 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT LIGHT CHAIN, RESIDUES 1-212 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#2: Antibody IGG FAB (IGG3, KAPPA) HEAVY CHAIN 291-2G3-A


Mass: 22933.863 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT HEAVY CHAIN, RESIDUES 1-213 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 543.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growpH: 8 / Details: 14 % PEG 3350, 50 MM TRIS PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 25, 2003 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→45.175 Å / Num. obs: 81582 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.2 / % possible all: 72

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZ6

1uz6


Resolution: 1.8→91.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.144 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4064 5 %RANDOM
Rwork0.21 ---
obs-77517 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å2-2.03 Å21.38 Å2
2---2.1 Å2-1.58 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 74 287 6975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226889
X-RAY DIFFRACTIONr_bond_other_d0.0010.026019
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9559393
X-RAY DIFFRACTIONr_angle_other_deg0.67314074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08124.022271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.485151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5791533
X-RAY DIFFRACTIONr_chiral_restr0.0760.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027549
X-RAY DIFFRACTIONr_gen_planes_other00.021360
X-RAY DIFFRACTIONr_nbd_refined0.2040.31064
X-RAY DIFFRACTIONr_nbd_other0.2160.35729
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.53981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.5558
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.543
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5441.55477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90526954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.78433122
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6584.52431
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 237
Rwork0.254 4630
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)
12.02912.23811.39433.11571.61073.57010.0119-0.2765-0.15210.6688-0.27940.12550.6268-0.34060.26750.1997-0.06720.0862-0.0551-0.0264-0.0755-4.6755-4.420916.6703
22.564-0.0516-1.89250.90720.46914.97820.4421-0.40040.27790.3601-0.1161-0.0909-0.54570.2703-0.3260.2718-0.02960.0691-0.0468-0.0217-0.1175-0.244212.702724.4274
31.83761.08750.18673.1297-0.87567.53020.21080.5317-0.09250.0928-0.18440.28660.2276-0.6937-0.02640.02650.10350.02460.0504-0.04-0.1186-6.54785.8049.0127
42.7778-1.0235-2.82110.37711.03942.8650.51760.38390.5790.8917-0.10860.7425-0.4494-0.8243-0.40910.07050.08480.10560.04420.01020.0291-11.32911.620918.0852
51.44350.92250.44962.20091.91376.33680.0179-0.039-0.09240.4946-0.36610.42610.2688-1.02610.34810.0701-0.03840.12360.0645-0.1021-0.0344-11.52380.807315.6943
64.40.2615-2.09725.3936.33548.76030.5311-0.38750.30730.498-0.0619-0.1089-0.38990.5513-0.46910.2252-0.03540.0529-0.0583-0.0192-0.13464.746712.764318.946
70.41280.28350.15012.0940.82341.22710.05530.0213-0.10430.4101-0.14180.10140.4437-0.24240.0865-0.0508-0.0446-0.06740.02180.02830.0327-1.1632-20.2846-9.0333
81.8448-2.0703-0.63468.4349-0.86012.3508-0.04880.16920.2036-0.3739-0.0258-0.6527-0.11290.20320.07460.0035-0.08270.1421-0.1435-0.008-0.06279.667947.334533.6588
93.31850.6871-2.1440.231-0.17643.7439-0.23480.1058-0.2823-0.63830.1771-0.14980.3445-0.12760.05770.4086-0.04410.1829-0.0209-0.0349-0.02296.076729.884726.3596
104.91710.1942-1.39247.08633.199.8460.13980.00880.3153-0.42320.01310.0114-0.6992-0.5382-0.15290.23290.06290.0714-0.18110.0359-0.203-2.462543.401634.6161
118.002-4.1462-15.28933.69816.502430.51360.32660.57121.5424-1.8252-0.11870.14050.7109-1.7415-0.20780.089-0.1681-0.07120.03020.06320.0209-2.250339.305723.5188
121.2353-0.0530.20555.18880.58922.0689-0.00720.2770.1303-0.4317-0.1072-0.093-0.3372-0.1340.11440.1950.00050.0837-0.15380.022-0.18052.811148.120728.384
131.11441.4478-3.52536.1654-1.603413.2205-0.2792-0.1163-0.1846-0.54120.2736-0.60430.42720.58420.00570.2595-0.01120.1893-0.1461-0.0349-0.08734.392928.344133.3893
140.5350.2047-0.08282.19210.4491.34730.0794-0.04490.134-0.27880.1451-0.4866-0.29710.1332-0.2245-0.0901-0.02050.0152-0.0679-0.01120.13015.378663.60858.707
155.241-1.6488-2.39463.10870.80541.77030.33210.1178-0.1290.2268-0.09960.0192-0.5796-0.0983-0.2325-0.11220.146-0.0466-0.1320.0222-0.2186.546414.6581-4.8659
160.1455-0.06441.26916.88710.540411.24580.3092-0.0250.26980.12160.02380.6143-1.0355-0.1985-0.3330.10830.20760.1475-0.18450.0704-0.0972-2.112624.24734.8809
174.80110.581-3.85510.34870.70448.0203-0.11710.0186-0.35220.36660.104-0.15990.25620.03890.01310.0490.0597-0.0375-0.10110.0115-0.14137.79437.6816.5391
186.6022-4.14351.05319.8653-1.51183.84530.3805-0.05460.18180.8726-0.1502-0.0561-0.75340.5474-0.23030.189-0.06720.0345-0.1263-0.0381-0.199111.465820.620210.1474
193.29620.0861-1.38832.77270.99042.56440.2212-0.05360.14810.37070.0425-0.1185-0.54310.1441-0.2637-0.02370.0625-0.0313-0.1080.0128-0.16849.999216.43320.8877
205.582-1.2495-2.21562.55454.928510.17850.30670.4446-0.23480.1-0.17890.5631-0.2766-0.6429-0.12780.05970.17920.12670.01050.0765-0.0569-5.71816.73968.6972
210.86260.81270.42811.56640.47420.80620.0361-0.0343-0.00320.0606-0.03630.15240.0365-0.16270.0002-0.18080.0492-0.08080.09820.01260.0962-0.7587-5.2076-16.0531
221.6323-0.22322.35412.2145-1.10146.18970.08120.05950.2298-0.4261-0.06480.0741-0.1581-0.4544-0.0165-0.13140.1305-0.09310.06920.0523-0.0106-12.210932.924150.0582
232.120.1673-3.43247.7521-0.37075.5585-0.09910.9584-0.0752-1.02970.29220.5956-0.0682-0.8571-0.19310.1541-0.0045-0.20.15820.042-0.1379-15.039328.511434.8446
242.94530.9737-2.57944.98890.63199.07760.0239-0.11850.0543-0.75850.3172-0.4963-0.69550.4371-0.3411-0.04580.03320.0461-0.0961-0.0082-0.0580.392333.694345.3525
2512.66063.33394.93087.69612.19828.5335-0.2958-0.0451-0.4007-0.63860.1938-0.6020.4978-0.2960.1020.04250.02530.0646-0.1553-0.0131-0.1219-3.988220.991141.2002
260.68690.5475-0.88513.4771.02074.5601-0.00850.1452-0.0604-0.30160.0286-0.0790.0441-0.4141-0.0201-0.10230.0421-0.0548-0.01070.0313-0.0692-8.021927.722947.9372
276.39-4.4654-4.95778.4242-0.6458.87550.16890.54920.3355-1.0132-0.09260.2335-0.0812-0.9086-0.07630.30350.0363-0.07580.10230.1083-0.1345-9.174735.035132.1288
280.27220.05810.0793.1055-0.42480.73310.02220.01680.1394-0.38510.04760.0048-0.21050.07-0.0699-0.08910.0576-0.0678-0.02260.03620.0585-9.095455.439659.2129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 23
2X-RAY DIFFRACTION2L24 - 34
3X-RAY DIFFRACTION2H1213 - 1215
4X-RAY DIFFRACTION3L35 - 49
5X-RAY DIFFRACTION4L50 - 56
6X-RAY DIFFRACTION5L57 - 88
7X-RAY DIFFRACTION6L89 - 97
8X-RAY DIFFRACTION7L98 - 212
9X-RAY DIFFRACTION8A1 - 23
10X-RAY DIFFRACTION9A24 - 34
11X-RAY DIFFRACTION9A1213 - 1215
12X-RAY DIFFRACTION10A35 - 49
13X-RAY DIFFRACTION11A50 - 56
14X-RAY DIFFRACTION12A57 - 88
15X-RAY DIFFRACTION13A89 - 97
16X-RAY DIFFRACTION14A98 - 212
17X-RAY DIFFRACTION15H1 - 26
18X-RAY DIFFRACTION16H27 - 35
19X-RAY DIFFRACTION17H36 - 49
20X-RAY DIFFRACTION18H50 - 66
21X-RAY DIFFRACTION19H67 - 94
22X-RAY DIFFRACTION20H95 - 104
23X-RAY DIFFRACTION21H105 - 213
24X-RAY DIFFRACTION22B1 - 26
25X-RAY DIFFRACTION23B27 - 35
26X-RAY DIFFRACTION24B36 - 49
27X-RAY DIFFRACTION25B50 - 66
28X-RAY DIFFRACTION26B67 - 94
29X-RAY DIFFRACTION27B95 - 104
30X-RAY DIFFRACTION28B105 - 213

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Yorodumi

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  • 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

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