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- PDB-6ev1: Crystal structure of antibody against schizophyllan -

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Basic information

Entry
Database: PDB / ID: 6ev1
TitleCrystal structure of antibody against schizophyllan
Components
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Schizophyllan
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.043 Å
AuthorsSung, K.H. / Josewski, J. / Dubel, S. / Blankenfeldt, W. / Rau, U.
CitationJournal: Sci Rep / Year: 2018
Title: Structural insights into antigen recognition of an anti-beta-(1,6)-beta-(1,3)-D-glucan antibody.
Authors: Sung, K.H. / Josewski, J. / Dubel, S. / Blankenfeldt, W. / Rau, U.
History
DepositionNov 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain
B: Light chain
C: Heavy chain
D: Light chain
E: Heavy chain
F: Light chain
G: Heavy chain
H: Light chain
I: Heavy chain
J: Light chain
K: Heavy chain
L: Light chain


Theoretical massNumber of molelcules
Total (without water)280,27212
Polymers280,27212
Non-polymers00
Water1629
1
A: Heavy chain
B: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-20 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: Heavy chain
D: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-21 kcal/mol
Surface area19570 Å2
MethodPISA
3
E: Heavy chain
F: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-20 kcal/mol
Surface area19460 Å2
MethodPISA
4
G: Heavy chain
H: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-18 kcal/mol
Surface area18970 Å2
MethodPISA
5
I: Heavy chain
J: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-20 kcal/mol
Surface area19370 Å2
MethodPISA
6
K: Heavy chain
L: Light chain


Theoretical massNumber of molelcules
Total (without water)46,7122
Polymers46,7122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-22 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.084, 112.832, 140.816
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Heavy chain


Mass: 23523.318 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
Light chain


Mass: 23188.732 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.41 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris, lithium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.04→56.416 Å / Num. obs: 55718 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.083 / Rrim(I) all: 0.155 / Net I/σ(I): 8.9
Reflection shellResolution: 3.043→3.096 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2768 / Rpim(I) all: 0.404 / Rrim(I) all: 0.764 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIM

1mim


Resolution: 3.043→56.416 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.2379 2690 4.83 %
Rwork0.1856 --
obs0.1882 55674 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.043→56.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19269 0 0 9 19278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419779
X-RAY DIFFRACTIONf_angle_d1.00326941
X-RAY DIFFRACTIONf_dihedral_angle_d2.77411763
X-RAY DIFFRACTIONf_chiral_restr0.0463012
X-RAY DIFFRACTIONf_plane_restr0.0063388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0431-3.09840.32911480.2892756X-RAY DIFFRACTION100
3.0984-3.1580.30771200.26352783X-RAY DIFFRACTION100
3.158-3.22250.28751430.25912820X-RAY DIFFRACTION100
3.2225-3.29260.30851220.25042764X-RAY DIFFRACTION99
3.2926-3.36910.32321190.25482808X-RAY DIFFRACTION99
3.3691-3.45340.28361460.23272764X-RAY DIFFRACTION99
3.4534-3.54670.2811390.21452798X-RAY DIFFRACTION100
3.5467-3.65110.24551450.21282784X-RAY DIFFRACTION99
3.6511-3.76890.26541560.20682790X-RAY DIFFRACTION100
3.7689-3.90360.26961550.18772743X-RAY DIFFRACTION100
3.9036-4.05980.2231470.17812781X-RAY DIFFRACTION100
4.0598-4.24450.20971330.15512790X-RAY DIFFRACTION100
4.2445-4.46820.22211570.14282790X-RAY DIFFRACTION99
4.4682-4.74810.19161350.1452815X-RAY DIFFRACTION99
4.7481-5.11440.17331390.13512784X-RAY DIFFRACTION99
5.1144-5.62870.23221700.15272792X-RAY DIFFRACTION99
5.6287-6.44220.22831420.16942793X-RAY DIFFRACTION99
6.4422-8.11260.23411360.18882800X-RAY DIFFRACTION99
8.1126-56.42570.20891380.182829X-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)
11.4581-0.11760.04551.54640.41711.40670.06880.4193-0.1668-0.2385-0.05490.25730.16160.0325-0.00440.25660.0065-0.00290.21750.02840.21376.6256-8.250844.1363
21.41440.399-0.18840.9642-1.15251.41320.1517-0.03790.19150.1623-0.03630.0847-0.19720.230.03010.22970.00150.03860.1206-0.02660.175238.740825.346358.2476
31.35780.8980.80840.62770.35791.40780.1016-0.6101-0.00720.2891-0.0424-0.16610.1566-0.09380.00020.40.07950.03520.52750.03770.371227.906-2.39979.0816
41.3843-0.04710.27911.6599-1.34611.1302-0.0474-0.3418-0.01040.1980.08530.1011-0.0592-0.07080.0280.21270.10080.03350.36110.01760.145634.532355.475831.8547
51.7036-0.72651.13751.72-1.0712.541-0.4156-0.12770.69910.1665-0.3212-0.5014-0.42310.259-1.2060.45340.1032-0.21180.4236-0.24580.5062-2.753730.2919-8.1702
61.60430.25420.37681.0874-0.05091.98230.0227-0.1056-0.29490.11020.1519-0.03840.1349-0.21720.00070.30450.02580.00380.22560.11330.354870.6671-7.042382.7763
70.50930.588-0.09951.75560.04730.60220.126-0.08440.250.2835-0.08420.08240.0371-0.1961-0.28020.21760.05120.0154-0.22280.11080.360214.47094.408756.3369
80.5446-0.00620.25881.066-0.69531.48570.1178-0.1336-0.1664-0.0591-0.16280.05430.31660.45610.0020.25520.07030.00430.27540.07320.215245.66448.726963.9606
90.68650.1488-0.40811.22450.28261.80540.0854-0.19860.09160.14960.0834-0.0728-0.30520.34640.02310.3254-0.02270.0260.3856-0.05440.189535.00033.4072-7.6751
100.7409-0.89060.1912.0344-0.261.28170.07380.21190.0716-0.30720.24020.22140.00380.02330.42420.2260.0819-0.12640.31620.1310.290626.643465.84517.8006
111.7038-1.2471.57032.148-0.74111.569-0.0474-0.17290.1939-0.1987-0.3522-0.2369-0.01570.4133-0.09140.3030.12080.0140.38360.02690.30284.494413.3586-6.2178
120.7206-0.5348-0.57160.6976-0.20491.8619-0.00270.2734-0.1751-0.12030.14240.0442-0.1802-0.0136-0.00020.2448-0.01210.03710.2703-0.00190.41377.8935-2.681366.2874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 3:217)
2X-RAY DIFFRACTION2(chain C and resseq 3:220)
3X-RAY DIFFRACTION3(chain E and resseq 3:218)
4X-RAY DIFFRACTION4(chain G and resseq 3:218)
5X-RAY DIFFRACTION5(chain I and resseq 4:218)
6X-RAY DIFFRACTION6(chain K and resseq 3:218)
7X-RAY DIFFRACTION7(chain B and resseq 3:210)
8X-RAY DIFFRACTION8(chain D and resseq 3:210)
9X-RAY DIFFRACTION9(chain F and resseq 3:212)
10X-RAY DIFFRACTION10(chain H and resseq 3:211)
11X-RAY DIFFRACTION11(chain J and resseq 3:212)
12X-RAY DIFFRACTION12(chain L and resseq 3:211)

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