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- PDB-2o5y: Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab progesteron... -

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Basic information

Entry
Database: PDB / ID: 2o5y
TitleCrystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab progesterone 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 / PROGESTERONE
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.85 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: Derived calculations / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE There is no aminoacid sequence database reference available for the protein. The protein ...SEQUENCE There is no aminoacid sequence database reference available for the protein. The protein was designed using variable domains from mouse and the constant domains from humans

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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)50,13216
Polymers48,5692
Non-polymers1,56314
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-148 kcal/mol
Surface area20600 Å2
MethodPISA, PQS
2
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)100,26432
Polymers97,1374
Non-polymers3,12728
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 area8490 Å2
ΔGint-310 kcal/mol
Surface area43700 Å2
MethodPISA
3
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)100,26432
Polymers97,1374
Non-polymers3,12728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area14220 Å2
ΔGint-334 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.354, 128.354, 91.816
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 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.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.59 Å3/Da / Density % sol: 73.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5 M ammonium sulfate, 0.15 M sodium citrate, 0.01% PEG 20000, pH 7.5, 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: 0.99996 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 21201 / Num. obs: 20438 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 11.1 / Net I/σ(I): 9.6
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.4 / Rsym value: 38.2 / % possible all: 88.3

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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: 2.85→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.89 / SU B: 24.013 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.443 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23586 1034 5.1 %RANDOM
Rwork0.18344 ---
all0.18607 19683 --
obs0.18607 19177 97.43 %-
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: 45.127 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å21.62 Å20 Å2
2--3.23 Å20 Å2
3----4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 88 65 3502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223522
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9764805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90124.593135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0215554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.889159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022604
X-RAY DIFFRACTIONr_nbd_refined0.2220.21421
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.26
X-RAY DIFFRACTIONr_mcbond_it0.5551.52203
X-RAY DIFFRACTIONr_mcangle_it1.05623524
X-RAY DIFFRACTIONr_scbond_it1.67331488
X-RAY DIFFRACTIONr_scangle_it2.7634.51281
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 73 -
Rwork0.276 1426 -
obs--98.3 %

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