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- PDB-4k3e: Crystal structure of bovine antibody BLV5B8 with ultralong CDR H3 -

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Basic information

Entry
Database: PDB / ID: 4k3e
TitleCrystal structure of bovine antibody BLV5B8 with ultralong CDR H3
Components
  • BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
  • BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CYSTINE KNOT / IMMUNE RECOGNITION
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
L(+)-TARTARIC ACID / IGL@ protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEkiert, D.C. / Wang, F. / Wilson, I.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Reshaping antibody diversity.
Authors: Wang, F. / Ekiert, D.C. / Ahmad, I. / Yu, W. / Zhang, Y. / Bazirgan, O. / Torkamani, A. / Raudsepp, T. / Mwangi, W. / Criscitiello, M.F. / Wilson, I.A. / Schultz, P.G. / Smider, V.V.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 2.0Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
L: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN
I: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
M: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5065
Polymers103,3564
Non-polymers1501
Water9,134507
1
H: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
L: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)51,6782
Polymers51,6782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-27 kcal/mol
Surface area22380 Å2
MethodPISA
2
I: BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN
M: BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8283
Polymers51,6782
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-26 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.612, 53.745, 330.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Antibody BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAIN


Mass: 29146.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGH / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAIN / IGL@ protein


Mass: 22531.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGL, IGL@ / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3T101
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDUE TO THE UNUSUAL LENGTH OF THE CDR H3 LOOP, ADDITIONAL CDR H3 RESIDUES BEYOND KABAT POSITION 100Z ...DUE TO THE UNUSUAL LENGTH OF THE CDR H3 LOOP, ADDITIONAL CDR H3 RESIDUES BEYOND KABAT POSITION 100Z WERE ACCOMMODATED AT POSITIONS 101 AND 102. THESE SEQUENCES REFER TO ANTIBODY CHAINS

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-sodium tartrate and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49527 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.1 / Net I/σ(I): 17.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.45 / % possible all: 75.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3D

4k3d


Resolution: 2.2→48.307 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 2525 5.13 %RANDOM
Rwork0.2024 ---
obs0.2043 49253 96.93 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 10 507 7520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047331
X-RAY DIFFRACTIONf_angle_d0.9489997
X-RAY DIFFRACTIONf_dihedral_angle_d10.9162593
X-RAY DIFFRACTIONf_chiral_restr0.0341168
X-RAY DIFFRACTIONf_plane_restr0.0031288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24230.3135950.25341857X-RAY DIFFRACTION70
2.2423-2.28810.281170.26142290X-RAY DIFFRACTION88
2.2881-2.33780.31271480.26312508X-RAY DIFFRACTION95
2.3378-2.39220.2561280.25292570X-RAY DIFFRACTION98
2.3922-2.4520.29581490.25282570X-RAY DIFFRACTION98
2.452-2.51830.28531530.24832582X-RAY DIFFRACTION99
2.5183-2.59240.26041440.24652632X-RAY DIFFRACTION99
2.5924-2.67610.29481490.23822624X-RAY DIFFRACTION100
2.6761-2.77170.2991280.23532634X-RAY DIFFRACTION99
2.7717-2.88270.25981450.22982677X-RAY DIFFRACTION100
2.8827-3.01390.29251520.2262645X-RAY DIFFRACTION100
3.0139-3.17280.29011470.22942674X-RAY DIFFRACTION100
3.1728-3.37150.26721440.20982671X-RAY DIFFRACTION100
3.3715-3.63170.2281560.19832691X-RAY DIFFRACTION100
3.6317-3.9970.20211230.17772695X-RAY DIFFRACTION100
3.997-4.5750.20211540.15242734X-RAY DIFFRACTION100
4.575-5.76260.1761390.14932767X-RAY DIFFRACTION100
5.7626-48.31810.2081540.20232907X-RAY DIFFRACTION99
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)
10.0502-0.1118-0.06080.16950.00190.1352-0.08220.4507-0.1747-0.0815-0.27150.062-0.36320.6467-0.25540.3522-0.220.15340.71310.0468-0.3273-8.70320.856615.4163
20.0102-0.0020.00880.00390.00640.0086-0.0683-0.06340.03120.31130.03640.12650.07420.1326-0.00010.52620.0720.04860.25590.0350.2176-33.64586.886-18.5481
30.00850.00820.03040.0169-0.04520.1281-0.03790.0598-0.0786-0.2163-0.0597-0.0447-0.04010.1085-0.05460.45280.0053-0.03410.5488-0.08050.1682-14.8866-4.37739.1312
40.1350.0269-0.03870.0796-0.03950.10460.0095-0.0837-0.16890.04770.0369-0.0356-0.0910.0913-00.2762-0.06720.0020.20260.0270.3145-3.9282-21.690538.4941
50.0290.0410.00490.0378-0.00470.02130.01980.1627-0.1883-0.06740.06620.11160.1576-0.0266-0.00010.5209-0.0211-0.13130.3839-0.06430.3598-26.9714-11.821112.2054
60.4660.1341-0.13150.1646-0.03860.15260.04070.1188-0.386-0.1950.02880.17550.05550.2547-0.06150.3031-0.0642-0.13770.1399-0.13070.2429-21.0855-18.436524.5488
70.0958-0.0173-0.020.08260.00760.0223-0.0292-0.0801-0.07830.0341-0.0730.2734-0.11860.0713-0.00010.2197-0.046-0.02850.19340.03420.3098-18.3469-24.505447.0351
80.06330.05040.03920.1472-0.0250.1057-0.053-0.33770.18670.03090.06880.1041-0.08320.1816-0.00310.2794-0.01360.06690.4416-0.0370.2452-12.18642.493868.1255
90.0176-0.0177-0.00080.01320.00820.0181-0.02560.0952-0.091-0.1216-0.0134-0.0589-0.0292-0.0467-00.33240.03330.03020.50850.01040.352-8.5905-21.7941103.426
100.06440.03160.02980.05020.03130.0296-0.1222-0.19140.1170.021-0.0684-0.05270.02140.0121-0.00710.2447-0.01780.05650.36240.06250.2041-16.2932-1.091664.6287
110.0960.06240.00760.19370.04890.224-0.05450.07780.0776-0.0289-0.25020.0917-0.22840.0662-0.05370.1651-0.05680.0120.24890.02760.3229-33.75689.235343.8309
120.02630.0263-0.00870.05040.0230.0382-0.0555-0.1101-0.13170.2404-0.02870.1860.13880.158100.38730.00860.07830.45040.14220.417-25.7982-15.207169.3835
130.07280.0402-0.02420.44410.19870.1901-0.0669-0.1319-0.0866-0.0182-0.0040.12090.04640.0493-0.19350.2187-0.03410.09080.27530.1020.3235-31.3742-9.251457.8517
140.09980.0123-0.01840.09440.07150.0458-0.0313-0.0485-0.0739-0.1250.0581-0.0803-0.04940.02-00.2636-0.07290.01430.20230.03540.3405-36.2603-4.842934.7183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and ( resid 2 through 100B )H2 - 100
2X-RAY DIFFRACTION2chain 'H' and ( resid 100C through 101M )H100 - 101
3X-RAY DIFFRACTION3chain 'H' and ( resid 101N through 109 )H101 - 109
4X-RAY DIFFRACTION4chain 'H' and ( resid 110 through 215 )H110 - 215
5X-RAY DIFFRACTION5chain 'L' and ( resid 2 through 48 )L2 - 48
6X-RAY DIFFRACTION6chain 'L' and ( resid 49 through 150 )L49 - 150
7X-RAY DIFFRACTION7chain 'L' and ( resid 151 through 212 )L151 - 212
8X-RAY DIFFRACTION8chain 'I' and ( resid 2 through 100B )I2 - 100
9X-RAY DIFFRACTION9chain 'I' and ( resid 100C through 101M )I100 - 101
10X-RAY DIFFRACTION10chain 'I' and ( resid 101N through 119 )I101 - 119
11X-RAY DIFFRACTION11chain 'I' and ( resid 120 through 215 )I120 - 215
12X-RAY DIFFRACTION12chain 'M' and ( resid 3 through 48 )M3 - 48
13X-RAY DIFFRACTION13chain 'M' and ( resid 49 through 150 )M49 - 150
14X-RAY DIFFRACTION14chain 'M' and ( resid 151 through 211 )M151 - 211

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