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- PDB-2o5x: Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diel... -

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Basic information

Entry
Database: PDB / ID: 2o5x
TitleCrystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM steroid-binding affinity
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
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.2Aug 30, 2023Group: 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_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 30, 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)49,74714
Polymers48,5692
Non-polymers1,17912
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-130 kcal/mol
Surface area19720 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)99,49528
Polymers97,1374
Non-polymers2,35824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13160 Å2
ΔGint-330 kcal/mol
Surface area37320 Å2
MethodPISA
3
L: chimeric antibody Fab 1E9-DB3
hetero molecules

L: chimeric antibody Fab 1E9-DB3
hetero molecules

H: chimeric antibody Fab 1E9-DB3
hetero molecules

H: chimeric antibody Fab 1E9-DB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,49528
Polymers97,1374
Non-polymers2,35824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_646y+1,x-1,-z+11
crystal symmetry operation2_545-y,x-y-1,z+1/31
crystal symmetry operation5_545x-y,-y-1,-z+2/31
Buried area6620 Å2
ΔGint-248 kcal/mol
Surface area43490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.573, 127.573, 91.928
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-411-

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.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 4.54 Å3/Da / Density % sol: 72.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.5 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: 0.99996 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 54755 / Num. obs: 54536 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 8.2 / Net I/σ(I): 15.6
Reflection shellResolution: 2.05→2.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Rsym value: 52.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C1E

1c1e


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.275 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20399 2730 5 %RANDOM
Rwork0.17812 ---
all0.17945 51644 --
obs0.17945 51412 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.637 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20.89 Å20 Å2
2--1.77 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 63 278 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223721
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.975121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60924.483145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15415602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.661512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022821
X-RAY DIFFRACTIONr_nbd_refined0.2020.21421
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.210
X-RAY DIFFRACTIONr_mcbond_it2.21532354
X-RAY DIFFRACTIONr_mcangle_it3.41853784
X-RAY DIFFRACTIONr_scbond_it6.00481558
X-RAY DIFFRACTIONr_scangle_it8.307111316
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 185 -
Rwork0.236 3758 -
obs--99.65 %
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)
16.55082.2456-0.18652.05390.6383.53260.1068-0.30710.34210.1711-0.10920.1918-0.1127-0.1990.0024-0.1938-0.0840.0459-0.1308-0.0351-0.164249.4553-42.867513.1555
22.01090.0927-0.66172.29722.856811.0628-0.08340.4756-0.0469-0.38010.0456-0.171-0.16860.77780.0378-0.2270.04520.0170.0640.028-0.212978.4576-45.9355-12.2953
32.4830.7328-1.79431.0148-0.85066.39880.01190.0850.0523-0.14390.00910.20890.104-0.3243-0.021-0.1869-0.1415-0.0114-0.11810.0122-0.198140.0337-56.0256-2.0351
45.6162-1.01573.44482.3201-1.10665.53850.11780.036-0.5906-0.04790.0438-0.29420.78040.5607-0.16160.00850.09210.0275-0.1541-0.0209-0.147369.8888-59.5541-11.0362
5197.8354-0.575483.2196537.6124390.527433.4081-1.13821.4087.00453.8746-0.30545.1203-4.0938-3.88621.44360.11190.0149-0.06750.05120.01320.058935.7014-51.54779.0281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1081 - 113
2X-RAY DIFFRACTION2LA109 - 213114 - 218
3X-RAY DIFFRACTION3HB1 - 1131 - 119
4X-RAY DIFFRACTION4HB114 - 227120 - 219
5X-RAY DIFFRACTION5HN3011

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