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- PDB-5jor: Crystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A -

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Basic information

Entry
Database: PDB / ID: 5jor
TitleCrystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A
Components
  • Fab 14.22 light chain
  • Fab14.22 heavy chain
KeywordsIMMUNE SYSTEM / S. pneumoniae serotype 14 / anti-glycan B cells / synthetic conjugate vaccine / nanomolar affinity anti-glycan antibody / immune system-bacterial glycan complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å
AuthorsSarkar, A. / Irimia, A. / Teyton, L. / Wilson, I.A.
CitationJournal: J. Clin. Invest. / Year: 2017
Title: T cells control the generation of nanomolar-affinity anti-glycan antibodies.
Authors: Polonskaya, Z. / Deng, S. / Sarkar, A. / Kain, L. / Comellas-Aragones, M. / McKay, C.S. / Kaczanowska, K. / Holt, M. / McBride, R. / Palomo, V. / Self, K.M. / Taylor, S. / Irimia, A. / ...Authors: Polonskaya, Z. / Deng, S. / Sarkar, A. / Kain, L. / Comellas-Aragones, M. / McKay, C.S. / Kaczanowska, K. / Holt, M. / McBride, R. / Palomo, V. / Self, K.M. / Taylor, S. / Irimia, A. / Mehta, S.R. / Dan, J.M. / Brigger, M. / Crotty, S. / Schoenberger, S.P. / Paulson, J.C. / Wilson, I.A. / Savage, P.B. / Finn, M.G. / Teyton, L.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fab14.22 heavy chain
A: Fab 14.22 light chain
F: Fab14.22 heavy chain
H: Fab14.22 heavy chain
L: Fab 14.22 light chain
C: Fab 14.22 light chain
D: Fab14.22 heavy chain
E: Fab 14.22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,29675
Polymers204,8578
Non-polymers8,43867
Water15,835879
1
B: Fab14.22 heavy chain
C: Fab 14.22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,82719
Polymers51,2142
Non-polymers2,61317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-105 kcal/mol
Surface area19310 Å2
MethodPISA
2
A: Fab 14.22 light chain
D: Fab14.22 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,80816
Polymers51,2142
Non-polymers1,59414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-83 kcal/mol
Surface area19630 Å2
MethodPISA
3
F: Fab14.22 heavy chain
E: Fab 14.22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,79525
Polymers51,2142
Non-polymers2,58123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-90 kcal/mol
Surface area19570 Å2
MethodPISA
4
H: Fab14.22 heavy chain
L: Fab 14.22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86615
Polymers51,2142
Non-polymers1,65213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-77 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.613, 75.992, 122.946
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 8 molecules BFHDALCE

#1: Antibody
Fab14.22 heavy chain


Mass: 26778.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody
Fab 14.22 light chain


Mass: 24436.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 946 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1:1 (v/v) protein/reservoir drop equilibrated against 3.6M ammonium sulfate, with 10% PEG400 and 10%MPD, in 1M of HEPES (pH 7.5) reservoir solution

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.206→49.74 Å / Num. obs: 109255 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.902 / Rsym value: 0.013 / Net I/σ(I): 6.1
Reflection shellResolution: 2.2061→2.2312 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
HKL-2000v706edata reduction
HKL-2000v706edata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGC

1qgc


Resolution: 2.206→49.733 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 5450 5 %
Rwork0.2052 --
obs0.2068 109097 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.206→49.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13202 0 440 879 14521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213987
X-RAY DIFFRACTIONf_angle_d0.5218959
X-RAY DIFFRACTIONf_dihedral_angle_d10.9038237
X-RAY DIFFRACTIONf_chiral_restr0.0422077
X-RAY DIFFRACTIONf_plane_restr0.0032353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2061-2.23120.32091580.29212847X-RAY DIFFRACTION81
2.2312-2.25740.33231720.27143347X-RAY DIFFRACTION97
2.2574-2.2850.32811710.27153396X-RAY DIFFRACTION98
2.285-2.31390.33341830.26783419X-RAY DIFFRACTION99
2.3139-2.34430.29721810.2753466X-RAY DIFFRACTION99
2.3443-2.37640.31820.26293474X-RAY DIFFRACTION100
2.3764-2.41040.33221830.26413455X-RAY DIFFRACTION100
2.4104-2.44640.29561790.25213479X-RAY DIFFRACTION100
2.4464-2.48460.30551830.25583420X-RAY DIFFRACTION100
2.4846-2.52530.28941810.24113502X-RAY DIFFRACTION100
2.5253-2.56890.31041920.24193457X-RAY DIFFRACTION100
2.5689-2.61560.2921840.24063495X-RAY DIFFRACTION100
2.6156-2.66590.27541800.23213441X-RAY DIFFRACTION100
2.6659-2.72030.24931840.23043493X-RAY DIFFRACTION100
2.7203-2.77940.32291830.22343462X-RAY DIFFRACTION100
2.7794-2.84410.2661920.21633468X-RAY DIFFRACTION100
2.8441-2.91520.25291780.20853481X-RAY DIFFRACTION100
2.9152-2.9940.2481730.21093478X-RAY DIFFRACTION100
2.994-3.08210.22611870.20723455X-RAY DIFFRACTION99
3.0821-3.18160.24451790.21093484X-RAY DIFFRACTION99
3.1816-3.29530.26611900.2113475X-RAY DIFFRACTION99
3.2953-3.42720.25681810.19883457X-RAY DIFFRACTION100
3.4272-3.58310.22591840.18623476X-RAY DIFFRACTION100
3.5831-3.77190.21441810.18173521X-RAY DIFFRACTION100
3.7719-4.00820.17841800.18153508X-RAY DIFFRACTION100
4.0082-4.31750.19061850.16463503X-RAY DIFFRACTION100
4.3175-4.75170.18431900.15493519X-RAY DIFFRACTION100
4.7517-5.43850.17181870.16833525X-RAY DIFFRACTION100
5.4385-6.84910.25961820.21663562X-RAY DIFFRACTION100
6.8491-49.74530.21911850.22273582X-RAY DIFFRACTION98
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)
15.597-0.46490.50060.5741-0.24522.0857-0.01390.1188-0.5115-0.05290.04110.07760.1979-0.2328-0.04880.4488-0.03330.03480.2090.0030.2125-15.4451-1.3354-24.4798
23.23560.9418-0.27270.4951-0.10840.6319-0.0733-0.0766-0.0303-0.04650.0422-0.00140.0111-0.0910.03080.35050.02470.00930.24040.01940.2152-14.16591.4472-6.7642
32.44460.03751.78430.47820.01821.5612-0.10390.21140.1397-0.0160.06910.1055-0.0753-0.01410.07280.3505-0.05110.03210.33690.03470.2373-23.987532.7574-30.4957
41.31920.18650.96480.7756-0.34942.3416-0.06420.09430.022-0.06410.0232-0.01990.0953-0.00940.03750.22670.00050.06010.25090.00780.2269-35.617820.0068-25.9244
51.2323-0.2081.00260.61440.09442.2278-0.0792-0.0340.04250.01770.0229-0.00430.10050.12120.03940.2450.00680.05710.2714-0.02310.2401-73.134720.6806-33.9948
62.8417-0.46031.74490.5837-0.2011.8018-0.1471-0.2440.16720.04010.0903-0.128-0.07320.00240.070.34490.04670.04280.3013-0.0460.2564-84.417533.2585-28.5963
73.49671.1792-0.69020.701-0.16270.8837-0.09350.0095-0.0953-0.06680.0774-0.03110.0649-0.10210.0180.35850.02160.01390.18580.03040.1907-2.08640.9033-65.5859
85.1018-0.03690.43570.41160.031.6906-0.01970.2078-0.5448-0.03790.06910.07690.3118-0.2326-0.07630.4593-0.06620.02330.23010.00540.2568-3.558537.0414-83.3021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D'
2X-RAY DIFFRACTION2chain 'A'
3X-RAY DIFFRACTION3chain 'H'
4X-RAY DIFFRACTION4chain 'L'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'C'
8X-RAY DIFFRACTION8chain 'B'

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