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- PDB-5tdo: Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 w... -

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Basic information

Entry
Database: PDB / ID: 5tdo
TitleCrystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Components
  • anti-HER2 Fab Heavy Chain
  • anti-HER2 Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin / Fab / 4D5
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsYin, Y. / Carter, P.J.
CitationJournal: To Be Published
Title: Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Authors: Yin, Y. / Carter, P.J.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-HER2 Fab Light Chain
B: anti-HER2 Fab Heavy Chain
C: anti-HER2 Fab Light Chain
D: anti-HER2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7787
Polymers94,5014
Non-polymers2763
Water8,161453
1
A: anti-HER2 Fab Light Chain
B: anti-HER2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4354
Polymers47,2512
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area19630 Å2
MethodPISA
2
C: anti-HER2 Fab Light Chain
D: anti-HER2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3433
Polymers47,2512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-25 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.948, 79.953, 86.124
Angle α, β, γ (deg.)113.810, 93.020, 102.380
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody anti-HER2 Fab Light Chain


Mass: 23463.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody anti-HER2 Fab Heavy Chain


Mass: 23787.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3,350, 0.04 M Citrate, 0.06 M BTP, pH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.61→24.071 Å / Num. obs: 113015 / % possible obs: 95.1 % / Redundancy: 2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.052 / Rrim(I) all: 0.074 / Net I/σ(I): 10.3 / Num. measured all: 225292
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.61-1.720.3720.715194
5.09-70.6720.0460.973197.5

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLM0.2.8data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVE

1fve


Resolution: 1.61→24.071 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.2671 5667 5.02 %
Rwork0.2366 --
obs0.2382 112922 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.13 Å2 / Biso mean: 27.3883 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.61→24.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6499 0 18 453 6970
Biso mean--44.53 28.36 -
Num. residues----853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076823
X-RAY DIFFRACTIONf_angle_d1.0979289
X-RAY DIFFRACTIONf_chiral_restr0.0421042
X-RAY DIFFRACTIONf_plane_restr0.0051198
X-RAY DIFFRACTIONf_dihedral_angle_d13.322451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.61-1.62830.3521800.28863568374894
1.6283-1.64740.32221850.28773459364494
1.6474-1.66750.32851910.2863509370094
1.6675-1.68860.35721750.28663646382194
1.6886-1.71080.30321800.2733504368494
1.7108-1.73430.34051870.28243533372094
1.7343-1.7590.31572040.26543565376994
1.759-1.78530.32811850.26743563374895
1.7853-1.81320.27451780.26153550372895
1.8132-1.84290.31441920.25163579377195
1.8429-1.87470.2961960.24543554375095
1.8747-1.90870.28611820.24943516369895
1.9087-1.94540.31161980.2473632383095
1.9454-1.98510.29251760.24773532370895
1.9851-2.02830.30162020.24093586378895
2.0283-2.07540.26421630.24263583374695
2.0754-2.12730.29641780.2333553373195
2.1273-2.18480.26951800.23763597377795
2.1848-2.2490.25141840.24183567375195
2.249-2.32160.27581970.23943586378395
2.3216-2.40450.26031950.24713577377296
2.4045-2.50060.29692140.24633550376495
2.5006-2.61430.28541930.24053650384396
2.6143-2.7520.26812040.24383599380396
2.752-2.92410.27281860.23653570375696
2.9241-3.14940.29441880.24363608379696
3.1494-3.46550.2461880.23423639382796
3.4655-3.96510.24791950.21943611380696
3.9651-4.98830.19691980.19193658385697
4.9883-24.07330.22261930.2223611380496
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)
11.20320.32171.07752.26031.66484.36510.0526-0.0414-0.00580.00440.02190.1058-0.0990.13990.04190.4325-0.09030.01110.2897-0.06640.199246.782154.860138.8763
21.35060.8749-0.78732.2362-1.09332.8690.2307-0.2093-0.14380.3012-0.2569-0.1772-0.29410.3634-0.02510.2494-0.1027-00.28140.01690.195536.223521.733352.3316
31.577-0.3021-0.19281.9866-0.03371.3422-0.0529-0.1382-0.03790.124-0.0010.0629-0.22050.0649-0.00820.0892-0.005-0.00690.11830.01090.101949.29943.644119.071
41.10190.013-0.32571.2797-0.08451.4050.0983-0.01940.00320.1117-0.03150.0465-0.0931-0.36120.01210.13350.01320.0110.29220.0230.151929.227522.426138.1167
51.2805-0.3106-0.1582.33941.49594.8233-0.0537-0.12140.01160.0486-0.0015-0.01210.41440.12590.00510.31650.0299-0.02980.2737-0.03720.182932.905424.3214-17.9048
60.7959-1.01370.16283.66320.03761.63980.1156-0.0543-0.1113-0.30390.05450.29940.0645-0.0464-0.01640.22660.028-0.05530.15570.00360.266343.2237-5.4662.6412
71.77890.1807-0.17381.7933-0.69951.8447-0.05010.07-0.0493-0.2643-0.0296-0.0098-0.02050.0738-0.01330.098-0.0038-0.00560.08950.00740.109430.670834.9661.4775
80.21230.06840.11421.59890.21881.33910.045-0.029-0.122-0.04770.2447-0.53920.05860.19360.33290.10980.01950.02810.165-0.08490.394850.1418.24139.5827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 2:108))A2 - 108
2X-RAY DIFFRACTION2chain 'A' and ((resseq 109:214))A109 - 214
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1:120))B1 - 120
4X-RAY DIFFRACTION4chain 'B' and ((resseq 121:220))B121 - 220
5X-RAY DIFFRACTION5chain 'C' and ((resseq 2:108))C2 - 108
6X-RAY DIFFRACTION6chain 'C' and ((resseq 109:214))C109 - 214
7X-RAY DIFFRACTION7chain 'D' and ((resseq 1:120))D1 - 120
8X-RAY DIFFRACTION8chain 'D' and ((resseq 121:220))D121 - 220

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