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- PDB-4s1d: Structure of IgG1 Fab fragment in complex with Biotincytidinamide -

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Basic information

Entry
Database: PDB / ID: 4s1d
TitleStructure of IgG1 Fab fragment in complex with Biotincytidinamide
Components
  • MAB M33 FAB FRAGMENT, heavy chain
  • MAB M33 FAB FRAGMENT, light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / hapten / MAB_M33_FAB_FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-41M
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDengl, S. / Hoffmann, E. / Grote, M. / Wagner, C. / Mundigl, O. / Georges, G. / Theorey, I. / Stubenrauch, K.-G. / Bujotzek, A. / Josel, H.-P. ...Dengl, S. / Hoffmann, E. / Grote, M. / Wagner, C. / Mundigl, O. / Georges, G. / Theorey, I. / Stubenrauch, K.-G. / Bujotzek, A. / Josel, H.-P. / Dziadek, S. / Benz, J. / Brinkmann, U.
CitationJournal: Faseb J. / Year: 2015
Title: Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies.
Authors: Dengl, S. / Hoffmann, E. / Grote, M. / Wagner, C. / Mundigl, O. / Georges, G. / Thorey, I. / Stubenrauch, K.G. / Bujotzek, A. / Josel, H.P. / Dziadek, S. / Benz, J. / Brinkmann, U.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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: MAB M33 FAB FRAGMENT, heavy chain
L: MAB M33 FAB FRAGMENT, light chain
C: MAB M33 FAB FRAGMENT, heavy chain
D: MAB M33 FAB FRAGMENT, light chain
E: MAB M33 FAB FRAGMENT, heavy chain
F: MAB M33 FAB FRAGMENT, light chain
O: MAB M33 FAB FRAGMENT, heavy chain
P: MAB M33 FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,16013
Polymers189,5788
Non-polymers1,5825
Water6,053336
1
H: MAB M33 FAB FRAGMENT, heavy chain
L: MAB M33 FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7663
Polymers47,3952
Non-polymers3711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-26 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: MAB M33 FAB FRAGMENT, heavy chain
D: MAB M33 FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7663
Polymers47,3952
Non-polymers3711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-26 kcal/mol
Surface area18920 Å2
MethodPISA
3
E: MAB M33 FAB FRAGMENT, heavy chain
F: MAB M33 FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7663
Polymers47,3952
Non-polymers3711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-30 kcal/mol
Surface area19290 Å2
MethodPISA
4
O: MAB M33 FAB FRAGMENT, heavy chain
P: MAB M33 FAB FRAGMENT, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8624
Polymers47,3952
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-40 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.094, 119.620, 96.181
Angle α, β, γ (deg.)90.00, 117.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
MAB M33 FAB FRAGMENT, heavy chain


Mass: 23773.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody
MAB M33 FAB FRAGMENT, light chain


Mass: 23621.037 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-41M / N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysinamide / N-epsilon-Biotinyl-lysine-amid


Mass: 371.498 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H29N5O3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15M ammonium sulfate, 0.1M MES, 15%PEG 4000, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→119 Å / Num. all: 74713 / Num. obs: 74645 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.29
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 3.53 % / Num. unique all: 3658 / Rsym value: 0.65 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DA+data collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished in house Fab fragment structure

Resolution: 2.5→119 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.428 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R: 0.966 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27446 3132 5 %RANDOM
Rwork0.22547 ---
obs0.22799 58977 99.91 %-
all-62797 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å24.17 Å2
2---2.72 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13109 0 105 336 13550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212206
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.94718512
X-RAY DIFFRACTIONr_angle_other_deg0.6413.00228231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63851690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18524.696543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.842152109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7841538
X-RAY DIFFRACTIONr_chiral_restr0.0580.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023062
X-RAY DIFFRACTIONr_mcbond_it1.1094.366796
X-RAY DIFFRACTIONr_mcbond_other1.1084.3596795
X-RAY DIFFRACTIONr_mcangle_it1.9296.5338474
X-RAY DIFFRACTIONr_mcangle_other1.9296.5348475
X-RAY DIFFRACTIONr_scbond_it0.9664.4036777
X-RAY DIFFRACTIONr_scbond_other0.8874.3666670
X-RAY DIFFRACTIONr_scangle_other1.5556.5269897
X-RAY DIFFRACTIONr_long_range_B_refined5.38333.86214352
X-RAY DIFFRACTIONr_long_range_B_other5.34233.714278
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 234 -
Rwork0.392 4353 -
obs--99.8 %
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)
10.7363-0.22730.0690.3946-0.86532.3198-0.09670.0221-0.04410.14250.0262-0.0406-0.1676-0.26560.07050.52970.0845-0.29440.4946-0.09440.180829.1592-33.527755.3877
21.2669-0.07280.63660.7522-0.86352.3811-0.0108-0.0121-0.1017-0.0692-0.05870.07960.2286-0.34870.06950.56050.0652-0.23410.5826-0.08620.178122.4354-50.236255.6086
31.1377-0.2187-0.15372.01-0.37231.88920.0946-0.00850.2636-0.1439-0.0194-0.1704-0.01730.3378-0.07520.3838-0.0257-0.14930.4644-0.05540.165316.0839-12.1785-7.2661
41.9470.4974-0.01831.8021-0.76632.5646-0.03770.47040.1128-0.3034-0.01370.2951-0.0368-0.3740.05130.55250.1295-0.28480.5946-0.05660.16410.0159-15.9707-15.4827
51.1902-0.12440.41970.98740.35342.16750.1017-0.04840.1808-0.2834-0.1511-0.1346-0.0843-0.19940.04940.23650.0046-0.07850.3291-0.00260.1525-43.2369-38.14340.4716
61.6398-0.27160.98461.81262.00164.35930.06560.09040.18670.0503-0.07750.08140.5375-0.04080.0120.1924-0.0495-0.07560.2957-0.09260.1229-40.1487-55.99931.3046
71.71531.5191-0.03512.6327-0.10350.51340.2117-0.3530.08210.5118-0.19390.1914-0.122-0.0301-0.01770.51330.0796-0.1130.5039-0.0210.0773-9.351-21.204343.2018
82.26931.4081-1.32011.7025-1.01811.90620.09880.02250.1640.1872-0.02240.3877-0.2178-0.2774-0.07640.26640.0733-0.14090.2593-0.05690.2615-25.0422-15.60437.0236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 220
2X-RAY DIFFRACTION2L1 - 213
3X-RAY DIFFRACTION3C2 - 220
4X-RAY DIFFRACTION4D1 - 211
5X-RAY DIFFRACTION5E1 - 219
6X-RAY DIFFRACTION6F1 - 213
7X-RAY DIFFRACTION7O1 - 220
8X-RAY DIFFRACTION8P1 - 210

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