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- PDB-5bmf: Crystal Structure of a Theophylline binding antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5bmf
TitleCrystal Structure of a Theophylline binding antibody Fab fragment
Components
  • Fab fragment heavy chain
  • Fab fragment light chain
KeywordsIMMUNE SYSTEM / antibody / hapten binding / theophylline
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-4TJ
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBujotzek, A. / Fuchs, A. / Changtao, Q. / Klostermann, S. / Benz, J. / Antes, I. / Dengl, S. / Hoffmann, E. / Georges, G.
CitationJournal: Mabs / Year: 2015
Title: MoFvAb: Modeling the Fv region of antibodies.
Authors: Bujotzek, A. / Fuchs, A. / Qu, C. / Benz, J. / Klostermann, S. / Antes, I. / Georges, G.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2May 1, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab fragment heavy chain
L: Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4083
Polymers48,3732
Non-polymers1,0351
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.438, 129.438, 92.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Fab fragment heavy chain


Mass: 24148.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Fab fragment light chain


Mass: 24224.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-4TJ / 2-(5-{1-[1-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)-4,15-dioxo-8,11-dioxa-5,14-diazaicosan-20-yl]-3,3-dimethyl-6-sulfo-1,3-dihydro-2H-indol-2-ylidene}penta-1,3-dien-1-yl)-1-ethyl-3,3-dimethyl-3H-indolium-5-sulfonate


Mass: 1035.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H66N8O12S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 2M Na-Formate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.8→112 Å / Num. obs: 22443 / % possible obs: 100 % / Redundancy: 8.6 % / Rsym value: 0.185 / Net I/σ(I): 3.9
Reflection shellResolution: 2.8→2.95 Å / Rsym value: 1.3

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Processing

Software
NameVersionClassification
PHENIXdev_1931refinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house Fab fragment coordinates

Resolution: 2.8→71.434 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1150 5.13 %
Rwork0.1864 --
obs0.1881 22413 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→71.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 27 76 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163440
X-RAY DIFFRACTIONf_angle_d1.2644690
X-RAY DIFFRACTIONf_dihedral_angle_d15.0031240
X-RAY DIFFRACTIONf_chiral_restr0.066522
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92750.40241270.31552635X-RAY DIFFRACTION100
2.9275-3.08190.34071670.29912591X-RAY DIFFRACTION100
3.0819-3.2750.31461750.26262602X-RAY DIFFRACTION100
3.275-3.52780.24881340.22492641X-RAY DIFFRACTION100
3.5278-3.88280.22111460.17692654X-RAY DIFFRACTION100
3.8828-4.44460.16691300.15132663X-RAY DIFFRACTION100
4.4446-5.59940.17691260.12962692X-RAY DIFFRACTION100
5.5994-71.45690.16821450.16662785X-RAY DIFFRACTION100
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)
10.3938-0.8619-0.05823.42610.17013.8929-0.3104-0.10860.02790.24590.05030.5767-0.4369-0.40910.11710.53070.00980.06270.561-0.05020.591450.1909-7.5818-7.682
23.51041.64991.40273.7148-2.24963.04770.148-0.4602-0.2164-0.2162-0.1267-0.4286-0.07620.37830.08890.48180.0377-0.02780.3585-0.04410.434460.693-10.7253-5.2275
31.23910.50690.7164.2460.73693.49130.0575-0.04430.13570.40530.1028-0.3296-0.1909-0.1439-0.13470.52870.0559-0.02070.4299-0.05020.432457.2356-6.2836-6.3644
41.2058-0.4663-0.29852.26630.4922.1203-0.38350.4047-0.0649-0.63121.00810.71980.6012-1.1813-0.05630.5904-0.1613-0.07830.46730.00270.644345.3799-34.8174-19.1771
51.79050.2874-1.19074.7802-1.47123.5608-0.0631-0.1127-0.03990.06660.51320.9636-0.0988-1.0113-0.25150.4618-0.02830.00080.80770.12390.651241.6794-34.5686-14.8364
63.17750.00960.41360.6168-0.99912.18860.0436-0.12910.01240.9571-0.2665-1.1912-0.32440.34690.17690.78890.0103-0.22270.64130.02670.7470.2431-19.97218.7074
72.0224-0.4814-1.29855.861-1.17682.80250.0301-0.3976-0.12591.097-0.0462-0.1597-0.2739-0.10650.04760.80480.0557-0.14120.5022-0.01120.511760.5202-22.41279.7506
80.84370.73610.09274.6615-1.1911.5159-0.03890.1223-0.0809-0.42370.1357-0.14310.4396-0.2179-0.00760.4284-0.00570.07410.548-0.03190.449855.2409-39.5985-10.0315
92.1542-0.4431-0.33324.6134-1.07454.2023-0.16440.3668-0.2291-1.16480.2040.10870.9529-0.0306-0.01190.8063-0.10920.05690.5469-0.03160.568253.1797-48.8464-17.0705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 53 )
3X-RAY DIFFRACTION3chain 'H' and (resid 54 through 109 )
4X-RAY DIFFRACTION4chain 'H' and (resid 110 through 137 )
5X-RAY DIFFRACTION5chain 'H' and (resid 138 through 216 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 37 )
7X-RAY DIFFRACTION7chain 'L' and (resid 38 through 95 )
8X-RAY DIFFRACTION8chain 'L' and (resid 96 through 155 )
9X-RAY DIFFRACTION9chain 'L' and (resid 156 through 216 )

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