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- PDB-5nbw: Crystal structure of the Fab fragment 22F12 in complex with 3-hyd... -

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Basic information

Entry
Database: PDB / ID: 5nbw
TitleCrystal structure of the Fab fragment 22F12 in complex with 3-hydroxybenzo[a]pyrene
Components
  • Fab 22F12 (A,B)
  • Fab 22F12 (L,H)
KeywordsIMMUNE SYSTEM / antibody / benzo[a]pyrene / Fab fragment / hapten
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / benzo[a]pyren-3-ol
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSkerra, A. / Eichinger, A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Tight Molecular Recognition of Benzo[a]pyrene by a High-Affinity Antibody.
Authors: Eichinger, A. / Neumaier, I. / Pschenitza, M. / Niessner, R. / Knopp, D. / Skerra, A.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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
L: Fab 22F12 (L,H)
H: Fab 22F12 (A,B)
A: Fab 22F12 (L,H)
B: Fab 22F12 (A,B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6096
Polymers96,0734
Non-polymers5372
Water4,360242
1
L: Fab 22F12 (L,H)
H: Fab 22F12 (A,B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0362
Non-polymers2681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area19620 Å2
MethodPISA
2
A: Fab 22F12 (L,H)
B: Fab 22F12 (A,B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0362
Non-polymers2681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-26 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.150, 81.000, 186.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B

NCS domain segments:

Component-ID: _ / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLA1 - 2141 - 214
21ASPASPAC1 - 2141 - 214
12GLUGLUHB1 - 2161 - 216
22GLUGLUBD1 - 2161 - 216

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab 22F12 (L,H)


Mass: 23950.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab 22F12 (A,B)


Mass: 24085.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-8SK / benzo[a]pyren-3-ol


Mass: 268.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.2 M Na-malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014 / Details: mirrors
RadiationMonochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→61.1 Å / Num. obs: 35232 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5049 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M1G

4m1g


Resolution: 2.4→61.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.963 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22795 1704 4.8 %RANDOM
Rwork0.18035 ---
obs0.18268 33462 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0 Å2
2--1.11 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 2.4→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 42 242 6920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.026866
X-RAY DIFFRACTIONr_bond_other_d0.0020.026146
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9519354
X-RAY DIFFRACTIONr_angle_other_deg1.055314270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6485856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34424.748278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.822151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9881520
X-RAY DIFFRACTIONr_chiral_restr0.1060.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2212.6293436
X-RAY DIFFRACTIONr_mcbond_other2.2062.6273435
X-RAY DIFFRACTIONr_mcangle_it3.8563.9254288
X-RAY DIFFRACTIONr_mcangle_other3.8573.9284289
X-RAY DIFFRACTIONr_scbond_it2.0712.7913430
X-RAY DIFFRACTIONr_scbond_other2.0662.793380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5074.0944991
X-RAY DIFFRACTIONr_long_range_B_refined5.90229.1067474
X-RAY DIFFRACTIONr_long_range_B_other6.00429.4337155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L133080.08
12A133080.08
21H125860.1
22B125860.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 124 -
Rwork0.274 2412 -
obs--98.87 %
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)
10.4658-0.1258-0.25480.10350.12630.4952-0.00320.1440.04210.0442-0.05320.0349-0.068-0.01080.05650.130.0147-0.0180.1134-0.01360.0555-9.0658-22.504318.902
20.49190.0762-0.46230.053-0.04060.51320.00160.06670.03870.00560.0050.04880.0282-0.0005-0.00660.1176-0.0085-0.0040.1039-0.00080.04845.5564-26.136928.2604
30.6251-0.283-0.55030.6920.90651.2562-0.01850.120.0209-0.0759-0.08830.0944-0.1017-0.14020.10680.14340.0173-0.03670.0635-0.00710.0232-9.306815.278914.5452
40.7162-0.4747-1.21770.37210.88432.1797-0.0923-0.15510.0406-0.00160.1367-0.00320.06120.3063-0.04440.1184-0.0387-0.00430.1022-0.01140.034.84712.033624.6674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 214
2X-RAY DIFFRACTION2H1 - 216
3X-RAY DIFFRACTION3A1 - 214
4X-RAY DIFFRACTION4B1 - 216

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