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- PDB-4x4x: Retrofitting antibodies with stabilizing mutations. Herceptin scF... -

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Basic information

Entry
Database: PDB / ID: 4x4x
TitleRetrofitting antibodies with stabilizing mutations. Herceptin scFv mutant.
Components
  • Human Variable Heavy Chain of Herceptin
  • Human Variable Light Chain of Herceptin
KeywordsIMMUNE SYSTEM / antibody stabilization mutations
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsLangley, D.B. / Roome, B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Retrofitting antibodies with stabilizing mutations
Authors: Langley, D.B. / Roome, B. / Christ, D.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Variable Heavy Chain of Herceptin
B: Human Variable Light Chain of Herceptin
C: Human Variable Heavy Chain of Herceptin
D: Human Variable Light Chain of Herceptin


Theoretical massNumber of molelcules
Total (without water)52,6004
Polymers52,6004
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-23 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.190, 91.190, 114.350
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 Human Variable Heavy Chain of Herceptin


Mass: 14565.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Antibody Human Variable Light Chain of Herceptin


Mass: 11734.021 Da / Num. of mol.: 2 / Mutation: S52D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: small hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3.5 M sodium formate, 100 mM sodium acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.25→35.65 Å / Num. obs: 26621 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0073refinement
RefinementResolution: 2.25→35.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 20.039 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26906 1329 5 %RANDOM
Rwork0.22618 ---
obs0.2283 25257 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 2.25→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 0 12 3149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023215
X-RAY DIFFRACTIONr_bond_other_d0.0010.022766
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9274399
X-RAY DIFFRACTIONr_angle_other_deg0.78836289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61922.81121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7831517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
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_it1.6632.9651729
X-RAY DIFFRACTIONr_mcbond_other1.6632.9651728
X-RAY DIFFRACTIONr_mcangle_it2.7074.4362149
X-RAY DIFFRACTIONr_mcangle_other2.7064.4362150
X-RAY DIFFRACTIONr_scbond_it1.7182.9751485
X-RAY DIFFRACTIONr_scbond_other1.7172.9751486
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6534.4252250
X-RAY DIFFRACTIONr_long_range_B_refined4.27123.5713406
X-RAY DIFFRACTIONr_long_range_B_other4.27123.5733407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 100 -
Rwork0.337 1827 -
obs--100 %
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)
11.38960.86540.2530.82330.62163.5616-0.22570.1627-0.1064-0.12060.2413-0.0145-0.46610.4132-0.01560.1824-0.10490.0240.20490.00770.023475.464661.775130.3557
22.3109-0.70570.59142.15560.86484.1650.15870.0687-0.0918-0.13540.04030.02560.00860.2343-0.19910.1369-0.10480.04170.1771-0.06340.032972.459249.1514113.1015
33.9791-0.60390.98432.1888-0.26933.3542-0.2258-0.12570.04830.11610.1175-0.0099-0.3203-0.10760.10830.15430.017-0.02870.0527-0.00490.006373.112260.6494153.6824
42.7002-0.66680.18772.32080.6092.76850.0764-0.22750.07030.2258-0.09310.0786-0.2295-0.25830.01670.43710.0298-0.11520.183-0.0550.060379.413470.0002172.6494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 118
2X-RAY DIFFRACTION2B1 - 106
3X-RAY DIFFRACTION3C2 - 118
4X-RAY DIFFRACTION4D1 - 106

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