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- PDB-3o2v: Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engi... -

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Basic information

Entry
Database: PDB / ID: 3o2v
TitleCrystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity
Components(Chimeric antibody Fab 1E9, ...) x 2
KeywordsIMMUNE SYSTEM / IgG antibody Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity
Authors: Verdino, P. / Aldag, C. / Jonsson, S. / Hilvert, D. / Wilson, I.A.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 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, light chain
H: Chimeric antibody Fab 1E9, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54928
Polymers48,5112
Non-polymers3,03826
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-166 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.730, 128.730, 92.342
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-242-

SO4

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Chimeric antibody Fab 1E9, light chain


Mass: 24082.904 Da / Num. of mol.: 1 / Mutation: F89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody Chimeric antibody Fab 1E9, heavy chain


Mass: 24428.510 Da / Num. of mol.: 1 / Mutation: L47T, M100bF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2

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Non-polymers , 4 types, 188 molecules

#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.55 Å3/Da / Density % sol: 72.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.75M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorDate: Jul 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39314 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.057 / Net I/σ(I): 20.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.557 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O5X

2o5x


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.581 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1973 5 %RANDOM
Rwork0.19225 ---
obs0.19362 37304 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.729 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.01 Å20 Å2
2--2.03 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 184 162 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223674
X-RAY DIFFRACTIONr_bond_other_d0.0020.022446
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9945019
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0035991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74124.653144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36715571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_nbd_refined0.1910.2499
X-RAY DIFFRACTIONr_nbd_other0.20.22342
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21657
X-RAY DIFFRACTIONr_nbtor_other0.0870.21951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.26
X-RAY DIFFRACTIONr_mcbond_it1.0551.52874
X-RAY DIFFRACTIONr_mcbond_other0.21.5901
X-RAY DIFFRACTIONr_mcangle_it1.35923681
X-RAY DIFFRACTIONr_scbond_it2.25131661
X-RAY DIFFRACTIONr_scangle_it2.9494.51328
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 151 -
Rwork0.277 2719 -
obs--99.79 %
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)
10.85991.3175-0.84347.51740.8233.8525-0.09220.02460.02290.4672-0.06460.4610.4364-0.02150.15680.01120.04430.103-0.37450.029-0.2054-66.572421.878528.6348
21.69160.3586-2.38722.23440.91310.8615-0.05980.33740.0936-0.40870.0445-0.0836-0.60930.4170.0153-0.117-0.1413-0.0197-0.15380.0689-0.2847-48.947144.79353.0841
31.55850.35590.54293.1664-1.83626.50360.09250.0667-0.17360.14650.00280.23360.2784-0.1007-0.0952-0.03650.11380.0399-0.4079-0.0086-0.249-60.74726.616313.1591
44.3261.41412.79323.14641.76376.86660.02060.0949-0.0060.12230.0741-0.6368-0.11651.165-0.0947-0.21020.10720.03650.03970.0368-0.2017-41.994330.43884.1926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 213
3X-RAY DIFFRACTION3H1 - 113
4X-RAY DIFFRACTION4H114 - 227

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