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

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Basic information

Entry
Database: PDB / ID: 5tdn
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: 1.63 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water10,539585
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 area4000 Å2
ΔGint-19 kcal/mol
Surface area19420 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 area3610 Å2
ΔGint-23 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.761, 79.597, 85.983
Angle α, β, γ (deg.)113.580, 93.060, 102.300
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


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


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
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: 1.63→23.506 Å / Num. obs: 108557 / % possible obs: 95.6 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 13.4 / Num. measured all: 212578 / Scaling rejects: 2
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / CC1/2: 0.717 / % possible all: 93.9

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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: 1.63→23.506 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2153 5444 5.02 %
Rwork0.1854 --
obs0.1869 108471 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.07 Å2 / Biso mean: 23.4495 Å2 / Biso min: 5.49 Å2
Refinement stepCycle: final / Resolution: 1.63→23.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6499 0 18 585 7102
Biso mean--45.75 27.93 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076793
X-RAY DIFFRACTIONf_angle_d1.0879243
X-RAY DIFFRACTIONf_chiral_restr0.0421037
X-RAY DIFFRACTIONf_plane_restr0.0051190
X-RAY DIFFRACTIONf_dihedral_angle_d13.1142439
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 (%)
1.63-1.64850.35061570.28523397355494
1.6485-1.66790.32681840.27323341352594
1.6679-1.68820.28771860.25483443362994
1.6882-1.70960.2831560.23153324348094
1.7096-1.73210.28441910.23593398358994
1.7321-1.75580.26961800.22563453363395
1.7558-1.78090.27941750.21793364353995
1.7809-1.80750.25221870.20593369355695
1.8075-1.83570.22641610.20173481364295
1.8357-1.86580.23151660.19653384355095
1.8658-1.89790.21891930.19673366355995
1.8979-1.93240.25451850.19173499368495
1.9324-1.96960.21011770.18743396357395
1.9696-2.00980.2241830.18723429361296
2.0098-2.05340.23471850.1933461364696
2.0534-2.10120.22561680.18733411357996
2.1012-2.15370.2241650.18593484364996
2.1537-2.21190.22551850.18983380356596
2.2119-2.27690.22252010.19343499370096
2.2769-2.35030.23391790.19863413359296
2.3503-2.43430.24442030.19613456365996
2.4343-2.53160.23451760.19173444362096
2.5316-2.64670.19722040.18773439364396
2.6467-2.7860.22062020.19063486368897
2.786-2.96030.21591920.19363484367697
2.9603-3.18830.23741850.19293479366497
3.1883-3.50820.19461710.18283519369097
3.5082-4.01370.18142050.16623465367097
4.0137-5.04860.15161910.13823487367897
5.0486-23.50810.20241510.16433476362796
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)
10.0953-0.0550.05260.16580.13880.1786-0.0366-0.1504-0.02660.08230.07470.1151-0.17770.09880.0750.4834-0.16960.05930.2549-0.15270.080543.509658.461939.4769
20.14020.1002-0.14680.1983-0.130.14950.1168-0.12710.00930.1924-0.1606-0.2514-0.13160.11680.00120.2836-0.04140.02730.20510.03320.199933.007825.281952.8612
30.22960.04470.11080.282-0.31460.8329-0.0395-0.107-0.03270.1917-0.03990.1404-0.29740.0274-0.10220.0378-0.00610.00610.08480.01460.126546.194347.081819.6491
40.07370.10490.02760.26920.03620.03970.0907-0.0817-0.050.09660.02960.0652-0.0439-0.45940.1520.09420.03320.06270.37740.0770.108326.185425.893138.7315
50.230.0623-0.13640.13760.1320.4906-0.1296-0.1351-0.021-0.07410.05740.11030.38420.097-0.28750.28370.0539-0.05420.1669-0.06450.050929.590927.4828-17.3256
60.1374-0.0897-0.00370.27310.03110.14790.01110.0088-0.0727-0.18250.05630.00410.1107-0.0095-0.00210.18140.0045-0.01630.11610.01590.207839.9779-1.90563.3949
70.21690.0262-0.01670.46760.00590.2901-0.043-0.0106-0.0025-0.20.0130.0120.04050.0835-0.04250.0736-0.0131-0.00430.07650.01160.100927.596138.30612.1088
80.0527-0.0455-0.04370.0683-0.04040.26630.0174-0.1187-0.15810.06280.1346-0.2003-0.04510.12590.12340.08130.02470.00970.1147-0.04460.272446.864711.78459.9193
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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