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- PDB-7kbp: Herceptin Diabody with R83T, E85C Mutations -

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Basic information

Entry
Database: PDB / ID: 7kbp
TitleHerceptin Diabody with R83T, E85C Mutations
ComponentsSingle-chain Fv
KeywordsPROTEIN BINDING / diabody / immunoglobin / reverse transcriptase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChesterman, C. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 AI027690 United States
CitationJournal: Structure / Year: 2021
Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry.
Authors: Chesterman, C. / Arnold, E.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-chain Fv
B: Single-chain Fv
C: Single-chain Fv
D: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,37421
Polymers104,8084
Non-polymers1,56617
Water5,981332
1
A: Single-chain Fv
hetero molecules

B: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,32512
Polymers52,4042
Non-polymers92110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area5800 Å2
ΔGint-33 kcal/mol
Surface area20660 Å2
MethodPISA
2
C: Single-chain Fv
hetero molecules

D: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0499
Polymers52,4042
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5430 Å2
ΔGint-29 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.153, 130.924, 139.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody
Single-chain Fv


Mass: 26202.109 Da / Num. of mol.: 4 / Mutation: R83T, E85C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 9% PEG 550 MME 0.1 M Bicine pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58592 / % possible obs: 99.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.182 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.001 / Num. unique obs: 2622 / CC1/2: 0.597 / Rrim(I) all: 1.093

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X4X

4x4x


Resolution: 2.3→49.9 Å / SU ML: 0.2866 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.1902 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 2444 4.97 %
Rwork0.1835 46719 -
obs0.1859 49163 83.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 102 332 7376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277207
X-RAY DIFFRACTIONf_angle_d0.49529805
X-RAY DIFFRACTIONf_chiral_restr0.04121071
X-RAY DIFFRACTIONf_plane_restr0.00321248
X-RAY DIFFRACTIONf_dihedral_angle_d5.15454110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.4028650.24611261X-RAY DIFFRACTION39.29
2.35-2.40.2954880.24631565X-RAY DIFFRACTION48.46
2.4-2.450.3488950.24161842X-RAY DIFFRACTION55.95
2.45-2.510.27081000.23831999X-RAY DIFFRACTION61.86
2.51-2.580.30741150.24912163X-RAY DIFFRACTION66.67
2.58-2.660.31271270.23572396X-RAY DIFFRACTION72.88
2.66-2.740.32731290.22742628X-RAY DIFFRACTION80.38
2.74-2.840.2931650.21592957X-RAY DIFFRACTION90.62
2.84-2.950.26181670.21373215X-RAY DIFFRACTION99.03
2.95-3.090.2631710.20493283X-RAY DIFFRACTION99.77
3.09-3.250.25831650.20323297X-RAY DIFFRACTION99.94
3.25-3.460.2381740.18793273X-RAY DIFFRACTION99.91
3.46-3.720.21561730.16963318X-RAY DIFFRACTION99.94
3.72-4.10.21671710.16623307X-RAY DIFFRACTION99.89
4.1-4.690.1791790.13233337X-RAY DIFFRACTION99.83
4.69-5.910.17861760.1473357X-RAY DIFFRACTION99.77
5.91-49.90.19521840.18863521X-RAY DIFFRACTION99.52

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