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- PDB-2o5z: Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-andr... -

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Basic information

Entry
Database: PDB / ID: 2o5z
TitleCrystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex
Components(chimeric antibody Fab 1E9-DB3) x 2
KeywordsIMMUNE SYSTEM / immunoglobulin / chimeric Fab / antibody engineering / evolution of ligand recognition
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 5-BETA-ANDROSTANE-3,17-DIONE
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.4 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Closely related antibody receptors exploit fundamentally different strategies for steroid recognition.
Authors: Verdino, P. / Aldag, C. / Hilvert, D. / Wilson, I.A.
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Dec 25, 2013Group: Non-polymer description / Refinement description
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: chimeric antibody Fab 1E9-DB3
H: chimeric antibody Fab 1E9-DB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,06626
Polymers48,5692
Non-polymers2,49824
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-268 kcal/mol
Surface area20100 Å2
MethodPISA, PQS
2
L: chimeric antibody Fab 1E9-DB3
H: chimeric antibody Fab 1E9-DB3
hetero molecules

L: chimeric antibody Fab 1E9-DB3
H: chimeric antibody Fab 1E9-DB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,13352
Polymers97,1374
Non-polymers4,99648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area17650 Å2
ΔGint-601 kcal/mol
Surface area37840 Å2
MethodPISA
3
H: chimeric antibody Fab 1E9-DB3
hetero molecules

H: chimeric antibody Fab 1E9-DB3
hetero molecules

L: chimeric antibody Fab 1E9-DB3
hetero molecules

L: chimeric antibody Fab 1E9-DB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,13352
Polymers97,1374
Non-polymers4,99648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
crystal symmetry operation3_654-x+y+1,-x,z-1/31
crystal symmetry operation4_655y+1,x,-z1
Buried area11520 Å2
ΔGint-543 kcal/mol
Surface area43970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.328, 127.328, 91.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11H-301-

SO4

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Components

#1: Antibody chimeric antibody Fab 1E9-DB3


Mass: 24143.002 Da / Num. of mol.: 1 / Fragment: light chain / Mutation: G63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-1E9 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody chimeric antibody Fab 1E9-DB3


Mass: 24425.525 Da / Num. of mol.: 1 / Fragment: heavy chain / Mutation: L47W, M87T, R100W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-1E9 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANO / 5-BETA-ANDROSTANE-3,17-DIONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 4.52 Å3/Da / Density % sol: 72.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0 M ammonium sulfate, 0.15 M sodium citrate, 0.01% PEG 20000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.05966 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05966 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 33879 / Num. obs: 33845 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 8.5 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.7 / Rsym value: 52.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: rigid body refinement / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.7 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 1562 5 %RANDOM
Rwork0.17145 ---
all0.17374 32190 --
obs0.17374 29534 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.053 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å21.62 Å20 Å2
2--3.25 Å20 Å2
3----4.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 136 174 3659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223642
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.994994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90724.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28215572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.481159
X-RAY DIFFRACTIONr_chiral_restr0.10.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022684
X-RAY DIFFRACTIONr_nbd_refined0.20.21406
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.28
X-RAY DIFFRACTIONr_mcbond_it1.79532253
X-RAY DIFFRACTIONr_mcangle_it3.12753616
X-RAY DIFFRACTIONr_scbond_it5.75781556
X-RAY DIFFRACTIONr_scangle_it7.753111369
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 87 -
Rwork0.26 1795 -
obs--76.29 %
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)
10.92690.5747-0.01742.98912.79289.31510.04410.140.111-0.07010.0357-0.2001-0.40520.1726-0.0798-0.05260.08280.002-0.37810.001-0.108759.1385-6.484-32.7076
23.78031.851-2.91424.1779-2.44796.52990.09670.0618-0.0115-0.11360.0550.7680.0523-1.1842-0.1517-0.24320.0344-0.06380.0735-0.0108-0.053140.9889-30.4822-41.7693
31.12211.82010.79549.47870.29133.3651-0.0457-0.0473-0.04010.3632-0.0134-0.4747-0.09840.11680.0591-0.10520.0471-0.0667-0.3261-0.0093-0.100965.7857-21.3755-17.5888
42.36910.13452.79931.8097-0.843611.9901-0.10980.3702-0.1154-0.53050.01510.08540.7846-0.42460.0947-0.0634-0.1710.0164-0.1563-0.0529-0.134848.4711-44.818-42.9529
5215.0684142.8622119.2586131.851585.715467.2727-1.1719-2.56911.98891.05390.3073-1.772-2.5758-3.19280.86460.15760.0769-0.07960.0119-0.05360.075467.5993-3.041-20.8054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1HB1 - 1131 - 119
2X-RAY DIFFRACTION2HB114 - 227120 - 219
3X-RAY DIFFRACTION3LA1 - 1081 - 113
4X-RAY DIFFRACTION4LA109 - 213114 - 218
5X-RAY DIFFRACTION5HZ5011

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