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- PDB-6foe: BaxB01 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 6foe
TitleBaxB01 Fab fragment
Components
  • Fab BaxB01 heavy chain
  • Fab BaxB01 light chain
KeywordsIMMUNE SYSTEM / IgG derived Fab / macrophage migration inhibitory factor / oxMIF form / PEPTIDE BINDING PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHollerweger, J. / Schinagl, A. / Kerschbaumer, R.J. / Scheiflinger, F. / Thiele, M. / Goettig, P. / Brandstetter, H.
CitationJournal: Biochemistry / Year: 2018
Title: Role of the Cysteine 81 Residue of Macrophage Migration Inhibitory Factor as a Molecular Redox Switch.
Authors: Schinagl, A. / Kerschbaumer, R.J. / Sabarth, N. / Douillard, P. / Scholz, P. / Voelkel, D. / Hollerweger, J.C. / Goettig, P. / Brandstetter, H. / Scheiflinger, F. / Thiele, M.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab BaxB01 heavy chain
B: Fab BaxB01 light chain
H: Fab BaxB01 heavy chain
L: Fab BaxB01 light chain


Theoretical massNumber of molelcules
Total (without water)94,6094
Polymers94,6094
Non-polymers00
Water1,45981
1
A: Fab BaxB01 heavy chain
B: Fab BaxB01 light chain


Theoretical massNumber of molelcules
Total (without water)47,3052
Polymers47,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-28 kcal/mol
Surface area19690 Å2
MethodPISA
2
H: Fab BaxB01 heavy chain
L: Fab BaxB01 light chain


Theoretical massNumber of molelcules
Total (without water)47,3052
Polymers47,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-28 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.700, 102.700, 188.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Fab BaxB01 heavy chain


Mass: 23759.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered Fab binds oxidized macrophage migration inhibitory factor (MIF)
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Fab BaxB01 light chain


Mass: 23545.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered Fab light chain binds oxidized macrophage migration inhibitory factor (MIF)
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 100 mM Tris/HCl, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 1, 2015 / Details: CRLs + KB mirror
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.6→72.62 Å / Num. obs: 31799 / % possible obs: 99.7 % / Redundancy: 17.4 % / Biso Wilson estimate: 52.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.049 / Rrim(I) all: 0.211 / Net I/av σ(I): 2.8 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.6-2.7416.41.960.445220.630.482.0221.9699.3
2.74-2.9116.31.2970.642920.3181.3391.29799.3
2.91-3.1115.90.7381.140460.1840.7630.73899.5
3.11-3.36150.4131.937950.1080.4280.413100
3.36-3.6815.10.256335280.0670.2650.256100
3.68-4.1117.70.1843.932130.0440.1890.184100
4.11-4.7521.40.1364.928360.030.1390.136100
4.75-5.8120.70.131524580.0290.1340.131100
5.81-8.2219.70.1225.119400.0280.1260.122100
8.22-72.6221.90.0914.811690.020.0930.09199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å70.75 Å
Translation2.7 Å70.75 Å

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Processing

Software
NameVersionClassification
XDSVersion May 1, 2016data reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9Q

4q9q


Resolution: 2.6→69.478 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.15
RfactorNum. reflection% reflection
Rfree0.2625 1537 4.85 %
Rwork0.2136 --
obs0.216 31694 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.65 Å2 / Biso mean: 64.2259 Å2 / Biso min: 22.87 Å2
Refinement stepCycle: final / Resolution: 2.6→69.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 0 81 6727
Biso mean---46.03 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046806
X-RAY DIFFRACTIONf_angle_d0.6759258
X-RAY DIFFRACTIONf_chiral_restr0.0431042
X-RAY DIFFRACTIONf_plane_restr0.0041182
X-RAY DIFFRACTIONf_dihedral_angle_d15.4382462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6840.39811240.30912688281299
2.684-2.77990.41771300.30392652278298
2.7799-2.89120.34781200.33982680280099
2.8912-3.02280.39291420.30062708285099
3.0228-3.18210.34881490.28226902839100
3.1821-3.38150.33661160.271427452861100
3.3815-3.64260.30461610.241527132874100
3.6426-4.00910.29641480.209627222870100
4.0091-4.58910.19221410.157627752916100
4.5891-5.78140.19281560.152928092965100
5.7814-69.5030.19231500.174629753125100
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)
14.0748-0.1983-0.04894.51270.34042.52040.03760.4363-0.649-0.2464-0.38710.76290.1334-0.77280.30230.349-0.02230.05380.6523-0.16470.58278.8411-1.6482-17.317
23.6133-2.26380.81213.8172-1.92573.3956-0.45940.6263-1.54070.1623-0.1234-0.16330.2030.33410.45210.6812-0.05280.34520.5475-0.13081.242329.9315-26.5722-14.1921
34.0013-0.99550.86853.53190.75423.5316-0.0124-0.3622-0.2240.4421-0.37170.97140.6047-0.5790.36680.5365-0.06720.24750.4954-0.13430.860230.1326-22.2258-10.2785
48.2158-0.59155.25334.3862-3.15748.60640.9833-0.2675-2.1926-0.0797-0.6840.16871.77810.4146-0.21340.98860.01550.25950.70610.10481.170929.0488-32.3121-7.125
54.191-1.0006-1.22963.39980.17262.7089-0.01610.0873-0.1219-0.1926-0.08010.0753-0.138-0.08360.08620.29370.02270.05870.3863-0.01020.233126.435910.4783-18.8976
60.9245-1.65220.37554.3146-0.73521.25760.02360.4314-0.66610.1352-0.3278-0.16220.1805-0.28960.34210.48860.0630.28190.4932-0.01710.775639.3737-19.9563-15.8977
70.66311.04241.02112.0311-0.19882.0589-0.18760.6463-0.481-0.886-0.0594-0.37780.26430.28530.26930.61270.01350.30820.5682-0.01850.818742.5745-20.6374-20.7818
80.6085-0.85490.67056.03681.47652.4847-0.20880.3448-0.4686-0.2247-0.2480.24540.39540.34010.45080.45510.08120.25020.71490.06840.724540.0987-17.8242-20.5302
91.9995-1.72390.00351.52890.37912.1841-0.35840.1638-1.045-1.3971-0.1777-0.35050.48380.36890.31830.83850.14520.34720.6325-0.04921.040741.3383-33.0471-22.7883
103.81731.841.96569.11673.96233.00810.23620.451-0.30591.0262-0.0119-1.26550.43220.2475-0.30070.65920.26840.31550.68730.11780.923349.7697-27.1673-17.6524
112.3329-0.407-0.78513.97810.57813.024-0.1146-0.25410.17330.06790.1638-0.3651-0.220.7423-0.0790.3034-0.0368-0.03980.5426-0.01270.31119.787338.2802-14.7207
124.2855-1.74670.53273.06821.78891.7234-0.20590.47690.715-0.47770.4951-0.1468-0.37951.1809-0.26690.5424-0.2206-0.0530.7445-0.03840.361717.515346.3066-17.7633
130.9926-1.0514-0.39421.18320.91972.8449-0.1298-0.15830.11340.05580.2994-0.1379-0.4380.722-0.09640.4082-0.0418-0.06340.552-0.0120.270113.048747.3305-9.3631
148.97561.8009-2.18717.4111-1.05837.62750.4261-0.871.39740.38310.09150.8591-1.3515-0.0182-0.60680.86110.0347-0.14370.4522-0.02370.4905-1.89364.7056.8007
154.23471.58021.23052.62380.69833.5294-0.47410.30360.2794-0.15920.3284-0.0068-0.50080.41910.04820.5195-0.0534-0.11090.3746-0.01290.3466.426158.26972.8878
160.0822-0.3504-0.10231.2350.34750.0908-0.199-1.50561.65840.6351-0.66081.0114-2.8007-0.95240.83132.03140.0635-0.12221.3634-0.88721.2442-0.49674.962216.9056
174.9624-1.5601-0.11862.43930.1572.24-0.0695-0.2277-0.01030.09420.0670.00350.19760.10290.02090.30330.0071-0.06530.2740.00830.2429-2.239234.6655-19.6619
181.27620.25170.10383.18591.56553.1931-0.24450.01090.6388-0.3771-0.02870.2843-1.2231-0.1110.26680.79560.0837-0.21810.4283-0.0330.5831-4.860966.3884-4.3879
198.10653.6905-0.46868.31790.34672.28010.7121-0.21411.04371.0947-0.36990.3491-0.7205-0.1423-0.33631.31760.2812-0.21760.5554-0.15550.8816-11.290874.38640.2005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 117 )A4 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 142 )A118 - 142
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 207 )A143 - 207
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 228 )A208 - 228
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 101 )B1 - 101
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 128 )B102 - 128
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 150 )B129 - 150
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 174 )B151 - 174
9X-RAY DIFFRACTION9chain 'B' and (resid 175 through 197 )B175 - 197
10X-RAY DIFFRACTION10chain 'B' and (resid 198 through 214 )B198 - 214
11X-RAY DIFFRACTION11chain 'H' and (resid 4 through 86 )H4 - 86
12X-RAY DIFFRACTION12chain 'H' and (resid 87 through 102 )H87 - 102
13X-RAY DIFFRACTION13chain 'H' and (resid 103 through 132 )H103 - 132
14X-RAY DIFFRACTION14chain 'H' and (resid 133 through 153 )H133 - 153
15X-RAY DIFFRACTION15chain 'H' and (resid 154 through 218 )H154 - 218
16X-RAY DIFFRACTION16chain 'H' and (resid 219 through 228 )H219 - 228
17X-RAY DIFFRACTION17chain 'L' and (resid 1 through 101 )L1 - 101
18X-RAY DIFFRACTION18chain 'L' and (resid 102 through 188 )L102 - 188
19X-RAY DIFFRACTION19chain 'L' and (resid 189 through 214 )L189 - 214

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