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- PDB-5ijv: Crystal structure of bovine Fab E03 -

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Basic information

Entry
Database: PDB / ID: 5ijv
TitleCrystal structure of bovine Fab E03
Components
  • bovine Fab E03 heavy chain
  • bovine Fab E03 light chain
KeywordsIMMUNE SYSTEM / antibody fab ultralong CDR H3
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: Sci Immunol / Year: 2016
Title: Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies.
Authors: Stanfield, R.L. / Wilson, I.A. / Smider, V.V.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Item: _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
L: bovine Fab E03 light chain
H: bovine Fab E03 heavy chain
A: bovine Fab E03 light chain
B: bovine Fab E03 heavy chain
C: bovine Fab E03 light chain
D: bovine Fab E03 heavy chain
E: bovine Fab E03 light chain
F: bovine Fab E03 heavy chain


Theoretical massNumber of molelcules
Total (without water)197,4588
Polymers197,4588
Non-polymers00
Water6,107339
1
L: bovine Fab E03 light chain
H: bovine Fab E03 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3642
Polymers49,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-29 kcal/mol
Surface area21250 Å2
MethodPISA
2
A: bovine Fab E03 light chain
B: bovine Fab E03 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3642
Polymers49,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-32 kcal/mol
Surface area21360 Å2
MethodPISA
3
C: bovine Fab E03 light chain
D: bovine Fab E03 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3642
Polymers49,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-31 kcal/mol
Surface area20920 Å2
MethodPISA
4
E: bovine Fab E03 light chain
F: bovine Fab E03 heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3642
Polymers49,3642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-33 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.244, 221.737, 67.947
Angle α, β, γ (deg.)90.00, 104.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
bovine Fab E03 light chain


Mass: 22548.611 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q3T101*PLUS
#2: Antibody
bovine Fab E03 heavy chain


Mass: 26815.846 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M NaCl 16.5% PEG 8000 0.1M phosphate-citrate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.2→49.1 Å / Num. obs: 89569 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k3d
Resolution: 2.2→49.1 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 3804 4.29 %
Rwork0.2043 --
obs0.2061 88706 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13567 0 0 339 13906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413882
X-RAY DIFFRACTIONf_angle_d0.6818955
X-RAY DIFFRACTIONf_dihedral_angle_d10.5428352
X-RAY DIFFRACTIONf_chiral_restr0.0482230
X-RAY DIFFRACTIONf_plane_restr0.0042411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.22790.33881010.2852140X-RAY DIFFRACTION68
2.2279-2.25720.30011530.27453164X-RAY DIFFRACTION100
2.2572-2.28810.26571330.27063177X-RAY DIFFRACTION100
2.2881-2.32080.3461460.26553172X-RAY DIFFRACTION100
2.3208-2.35550.33521470.26833190X-RAY DIFFRACTION100
2.3555-2.39230.31391250.26213204X-RAY DIFFRACTION100
2.3923-2.43150.29021470.25333153X-RAY DIFFRACTION100
2.4315-2.47340.28771580.25733181X-RAY DIFFRACTION100
2.4734-2.51840.30131360.26453199X-RAY DIFFRACTION100
2.5184-2.56680.35611400.25523157X-RAY DIFFRACTION100
2.5668-2.61920.29671460.25253178X-RAY DIFFRACTION100
2.6192-2.67620.28621300.2453181X-RAY DIFFRACTION100
2.6762-2.73840.3491430.24993202X-RAY DIFFRACTION100
2.7384-2.80690.27171420.23623159X-RAY DIFFRACTION100
2.8069-2.88280.31471420.22463153X-RAY DIFFRACTION100
2.8828-2.96760.31681440.22893226X-RAY DIFFRACTION100
2.9676-3.06340.25431410.22293167X-RAY DIFFRACTION100
3.0634-3.17280.26581400.22533161X-RAY DIFFRACTION100
3.1728-3.29980.27011440.22453206X-RAY DIFFRACTION100
3.2998-3.450.2431410.21913196X-RAY DIFFRACTION100
3.45-3.63180.26591410.20053183X-RAY DIFFRACTION100
3.6318-3.85930.24371400.19473174X-RAY DIFFRACTION100
3.8593-4.15710.2091430.17973190X-RAY DIFFRACTION100
4.1571-4.57520.18611450.15163172X-RAY DIFFRACTION100
4.5752-5.23660.1811490.14293223X-RAY DIFFRACTION100
5.2366-6.5950.18451450.17043181X-RAY DIFFRACTION100
6.595-49.11220.20631420.1723213X-RAY DIFFRACTION99
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)
15.11770.9238-0.61054.9513-0.04022.275-0.06340.0415-0.2698-0.23460.1785-0.5793-0.07940.058-0.08380.304-0.0130.02460.2223-0.00680.327344.795311.154327.4216
23.6479-0.19930.39660.2534-0.41741.1761-0.0018-0.09770.05920.3263-0.0736-0.08320.0669-0.00510.03310.2052-0.0470.04210.3114-0.04860.253669.736-10.239825.3624
34.46710.6931.15166.0922-0.11142.6293-0.02310.10640.0051-0.4452-0.0146-0.1304-0.02810.08150.05160.2276-0.00610.05160.26910.00580.279476.2666-12.575520.9752
42.8095-1.4104-0.8465.91351.51341.5397-0.1265-0.0808-0.4406-0.02190.06430.1940.06330.00730.07840.2734-0.0076-0.02430.28920.04180.434434.0082-7.348525.0578
58.5137-1.21881.39852.85742.86633.920.4766-0.22691.23310.298-0.6513-0.1062-0.2336-0.49070.2820.6321-0.0928-0.00810.5870.08161.688911.78830.568435.8151
61.7179-2.5779-0.48694.08180.62970.47910.04930.0992-0.022-0.0089-0.1550.1303-0.0656-0.05720.08070.2959-0.01750.00630.35620.04620.4837.3525-3.03925.5321
73.7981.52031.1333.55180.67945.6170.0702-0.16620.20040.3266-0.0703-0.1877-0.19760.28260.01460.26130.0029-0.00080.2196-0.02240.332363.1012-18.976430.2008
86.808-1.4480.54524.1907-0.67492.2990.00170.3529-0.4674-0.0870.080.10340.107-0.1364-0.00180.2485-0.0123-0.02510.2251-0.04770.220762.1389-79.088527.2256
91.2116-1.44990.65713.4621-0.30570.26750.06760.03870.049-0.0955-0.08690.0289-0.01260.0438-0.00810.2411-0.02840.03180.3452-0.00640.068353.5132-56.536222.0096
102.70110.6042-0.15243.8246-1.48164.3826-0.07660.2758-0.1116-0.17920.0129-0.17320.2096-0.09580.04380.19120.02010.0520.2979-0.04320.146649.4936-53.491318.3668
110.9906-0.1143-0.21478.5341-0.5060.39040.07720.02490.2042-0.5020.0145-0.1377-0.01290.0792-0.12860.3183-0.0107-0.07730.356-0.03130.440280.4355-69.647531.0142
121.8119-3.09990.33515.4692-1.20420.86790.19070.20270.0028-0.2357-0.2933-0.21620.18780.02190.05290.2451-0.0422-0.01830.2932-0.04390.351567.4927-64.206525.9118
134.32870.3624-0.70495.53440.02833.06350.01160.03870.06860.6606-0.1210.5963-0.0838-0.47980.05070.3327-0.00880.08430.3115-0.0110.179249.1329-38.362330.0993
144.65642.5805-0.20315.5762-0.25543.225-0.0972-0.40591.3225-0.1385-0.0562-0.1069-0.2245-0.01890.08370.30380.01760.0170.3364-0.12140.77835.6563-17.806953.7258
153.13870.368-0.37790.1859-0.4450.88440.1524-0.16020.20680.268-0.16690.29110.02980.28550.07550.2496-0.02320.06270.4274-0.02210.304760.783-39.915554.9773
163.35331.6433-0.13934.0144-2.06552.83540.0233-0.05030.0124-0.5958-0.2114-0.19990.31290.30410.20030.2920.07520.05920.46440.04780.283266.6944-42.496751.0695
176.5617-1.3761-0.83638.2555-0.66571.0217-0.113-0.377-0.090.2666-0.23780.18680.4247-0.3107-0.10060.23460.04060.00770.39190.01640.310431.0847-45.94753.7894
184.6337-0.20640.39886.9193-0.46720.92960.0019-0.7527-0.00431.07760.0018-0.0952-0.1463-0.1174-0.10630.36580.03290.04090.48220.02590.157125.5238-37.31260.0767
195.2039-1.5640.12425.59550.29321.11840.0747-0.26130.3094-0.23330.12080.3290.0063-0.176-0.19330.27170.02190.01630.36810.02870.242822.8944-34.25552.812
200.91841.4706-1.69832.7728-3.88636.5926-0.7667-0.409-0.2708-0.4082-1.35540.3016-0.48580.06972.50381.7176-0.0045-0.13961.30950.02931.22784.71411.825158.5058
213.3218-2.61570.33852.4991-0.70351.0524-0.3317-0.24830.81880.57530.07720.9253-0.6913-0.43160.36170.57760.139-0.07930.6982-0.24131.427912.7955-11.518156.4646
226.3552-4.34980.44135.6107-1.45150.53310.0486-0.34920.0846-0.36650.1321-0.43960.0434-0.0477-0.16070.31070.01360.05930.41770.03120.149639.3341-48.357150.3589
237.32213.07820.88858.05912.23335.10260.2781-0.06660.10210.41540.2708-0.3879-0.03651.0699-0.67770.2535-0.01680.05710.5905-00.242259.5742-50.59560.73
246.64832.13190.49175.3599-2.12241.2933-0.1527-0.01331.1490.052-0.11290.45570.0123-0.21470.12440.26580.01220.05360.31830.03980.339350.624-45.730557.7973
256.5333.4068-0.63084.00593.09415.5370.6079-1.02550.68830.5257-0.2101-0.119-0.20830.6341-0.36630.3404-0.06930.01130.579-0.07350.412855.8426-47.087365.8823
261.04261.6757-1.22975.3440.87594.68410.5754-1.2012-0.17390.5868-0.4366-0.45670.10520.1094-0.11620.2671-0.09150.0840.49530.05760.208453.7085-54.096464.6262
273.4624-0.8003-1.73521.7408-1.65514.8206-0.05270.1368-0.1228-1.08430.23210.89430.2236-0.7383-0.04231.3166-0.0881-0.44020.7879-0.06121.001144.9982-104.29468.4773
281.0858-1.4213-1.55561.8771.94832.0751-0.13730.26690.0146-0.8062-0.20130.2498-0.6103-0.1110.38042.64630.1181-0.17440.7455-0.02091.325557.4506-111.130764.687
295.8542.6091-2.84057.15492.51453.79580.4725-0.1806-1.276-1.1038-0.78570.82321.1340.8590.25511.2220.3841-0.31120.5966-0.02910.64456.4736-98.408974.5066
301.6608-0.09040.44290.082-0.02160.1379-0.8332-0.0524-0.478-0.2672-0.23410.64421.0951-0.41710.60911.3520.0194-0.08760.91980.24980.872256.9472-108.556180.0474
311.2704-1.655-1.852.26072.45212.6781-0.72650.0035-0.4942-0.78670.20950.0554-0.4101-0.80230.5671.9815-0.0858-0.32610.75770.16871.175252.6875-112.327170.2241
322.8997-3.02631.68358.1690.07131.69690.0662-0.45810.4813-1.50480.46940.35580.80250.0025-0.59861.4058-0.0038-0.4370.6156-0.11441.147449.9998-100.986674.0364
333.048-1.9641-3.27775.36632.78964.9935-0.70990.41350.1347-1.01010.4381-0.27521.65651.08780.13942.19960.5443-0.29980.962-0.07190.739165.3744-104.445162.0452
342.1641-2.37091.95254.6387-2.09873.36431.1457-0.7225-1.39640.50610.33930.41921.4493-0.7136-1.25290.8644-0.2182-0.37890.79670.19331.100136.9653-95.401870.0145
355.40120.06750.03833.6623-0.1373.6410.23940.6615-1.0037-0.2961-0.06630.00290.58180.134-0.0650.35370.0638-0.04810.4936-0.16380.400939.2425-81.502953.5977
360.84340.0328-0.41583.4681-0.48780.76680.39840.6138-0.1108-0.2806-0.5013-0.26891.1991.4519-0.17441.0130.57790.08981.2370.17481.001371.9755-89.683966.2264
370.8994-1.2389-0.18394.0261-0.36560.197-0.3036-0.0506-0.11230.0704-0.041-0.70420.52050.18950.24790.76090.19230.20480.59840.0850.498259.2682-93.27164.6578
385.20221.42530.1686.08-0.36834.2691-0.04470.01090.6756-0.0466-0.26870.97430.1811-0.56140.00180.2407-0.02020.06530.4951-0.10180.122536.8981-64.87363.1721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 3 through 101 )
2X-RAY DIFFRACTION2chain 'L' and (resid 102 through 129 )
3X-RAY DIFFRACTION3chain 'L' and (resid 130 through 211 )
4X-RAY DIFFRACTION4chain 'H' and (resid 2 through 105 )
5X-RAY DIFFRACTION5chain 'H' and (resid 106 through 125 )
6X-RAY DIFFRACTION6chain 'H' and (resid 126 through 155 )
7X-RAY DIFFRACTION7chain 'H' and (resid 156 through 249 )
8X-RAY DIFFRACTION8chain 'A' and (resid 3 through 92 )
9X-RAY DIFFRACTION9chain 'A' and (resid 93 through 139 )
10X-RAY DIFFRACTION10chain 'A' and (resid 140 through 211 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 251 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 101 )
15X-RAY DIFFRACTION15chain 'C' and (resid 102 through 129 )
16X-RAY DIFFRACTION16chain 'C' and (resid 130 through 211 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 17 )
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 39 )
19X-RAY DIFFRACTION19chain 'D' and (resid 40 through 104 )
20X-RAY DIFFRACTION20chain 'D' and (resid 105 through 117 )
21X-RAY DIFFRACTION21chain 'D' and (resid 118 through 139 )
22X-RAY DIFFRACTION22chain 'D' and (resid 140 through 155 )
23X-RAY DIFFRACTION23chain 'D' and (resid 156 through 181 )
24X-RAY DIFFRACTION24chain 'D' and (resid 182 through 211 )
25X-RAY DIFFRACTION25chain 'D' and (resid 212 through 235 )
26X-RAY DIFFRACTION26chain 'D' and (resid 236 through 251 )
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 18 )
28X-RAY DIFFRACTION28chain 'E' and (resid 19 through 33 )
29X-RAY DIFFRACTION29chain 'E' and (resid 34 through 48 )
30X-RAY DIFFRACTION30chain 'E' and (resid 49 through 61 )
31X-RAY DIFFRACTION31chain 'E' and (resid 62 through 75 )
32X-RAY DIFFRACTION32chain 'E' and (resid 76 through 91 )
33X-RAY DIFFRACTION33chain 'E' and (resid 92 through 101 )
34X-RAY DIFFRACTION34chain 'E' and (resid 102 through 113 )
35X-RAY DIFFRACTION35chain 'E' and (resid 114 through 211 )
36X-RAY DIFFRACTION36chain 'F' and (resid 3 through 87 )
37X-RAY DIFFRACTION37chain 'F' and (resid 88 through 213 )
38X-RAY DIFFRACTION38chain 'F' and (resid 214 through 251 )

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