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- PDB-6ao0: CAT192 Fab Insertion Mutant H2/L2 -

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Basic information

Entry
Database: PDB / ID: 6ao0
TitleCAT192 Fab Insertion Mutant H2/L2
Components
  • CAT192 Fab Heavy chain
  • CAT192 Fab Light chain
KeywordsIMMUNE SYSTEM / Fab / TGF-Beta / protein engineering / antibody engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLord, D.M. / Wei, R.R.
CitationJournal: MAbs / Year: 2018
Title: Structure-based engineering to restore high affinity binding of an isoform-selective anti-TGF beta 1 antibody.
Authors: Lord, D.M. / Bird, J.J. / Honey, D.M. / Best, A. / Park, A. / Wei, R.R. / Qiu, H.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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
L: CAT192 Fab Light chain
H: CAT192 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4687
Polymers47,9882
Non-polymers4805
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-66 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.060, 86.590, 45.890
Angle α, β, γ (deg.)90.000, 100.570, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-367-

HOH

21H-491-

HOH

31H-518-

HOH

41H-519-

HOH

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Components

#1: Antibody CAT192 Fab Light chain


Mass: 23281.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CAT192 Fab Heavy chain


Mass: 24706.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M Ammonium sulfate, 0.1M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.35→31.237 Å / Num. obs: 16303 / Biso Wilson estimate: 27.15 Å2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7335 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
CrystalCleardata collection
SCALAdata scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AMJ

6amj


Resolution: 2.35→31.237 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 768 4.71 %
Rwork0.2057 15535 -
obs0.2082 16303 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.19 Å2 / Biso mean: 33.8855 Å2 / Biso min: 9.5 Å2
Refinement stepCycle: final / Resolution: 2.35→31.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 25 204 3464
Biso mean--65.11 29.88 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023330
X-RAY DIFFRACTIONf_angle_d0.4834532
X-RAY DIFFRACTIONf_chiral_restr0.041506
X-RAY DIFFRACTIONf_plane_restr0.004577
X-RAY DIFFRACTIONf_dihedral_angle_d11.7321952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.53140.30891420.27572890303287
2.5314-2.7860.32561670.26263087325493
2.786-3.18880.2761540.23393124327894
3.1888-4.01620.24741550.18283177333295
4.0162-31.23940.22041500.17023257340796
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)
12.36030.65120.54532.39820.5622.8562-0.05560.10750.0952-0.0385-0.0682-0.0531-0.17020.05060.07930.113-0.02420.01290.11140.0350.22385.57112.2644-9.254
23.6463-1.21962.83170.4402-0.9672.21240.04190.2696-0.44350.3646-0.07660.0263-0.25930.7710.00050.3093-0.11650.02760.464-0.05990.75326.199711.9379-1.583
35.0268-1.28530.1952.5293-0.22572.2-0.0369-0.21160.32710.05660.0018-0.46530.09430.53610.06580.17970.05330.0050.39860.01120.38531.6394-4.152517.5928
41.7009-1.14860.82815.8747-3.91325.7871-0.0269-0.777-0.68630.19420.4360.8041-0.005-0.6974-0.38790.2647-0.18730.04790.3248-0.01860.2417-18.1492-18.07910.2933
51.4082-1.14110.65341.3816-0.43563.0327-0.0179-0.15740.120.0117-0.16830.09960.4097-0.32130.11890.1707-0.11230.02690.13030.01470.2201-17.4785-14.998-1.571
67.98191.30062.87771.25490.77622.6053-0.0046-0.27160.04460.3467-0.06530.34850.2154-0.23840.09560.2116-0.04070.04140.14480.04940.3756-17.8916-21.9193-0.0061
72.5442.25991.13957.33850.86834.39520.18130.2720.08470.72330.03120.3160.01290.4644-0.20460.1361-0.08050.01840.26610.06760.2595-9.6465-18.16717.2487
81.1869-0.05021.0811-0.0094-0.37283.1333-0.1405-0.1787-0.0190.13550.0618-0.0067-0.1285-0.27790.08380.2759-0.04730.06460.1098-0.04180.2614-10.0604-8.82486.8029
92.48130.34780.54694.2323-0.30164.5218-0.0745-0.25430.26990.29460.21930.0271-0.18530.2225-0.15040.16330.03370.01340.1907-0.06760.311718.2172-0.584522.8088
102.17240.0071-0.73354.27290.65863.2202-0.0238-0.21320.71630.44120.2149-0.8226-0.2221-0.0611-0.08880.08870.0665-0.01570.153-0.00610.391917.7708-2.954715.9889
114.06210.17570.92865.30071.09036.76190.1447-0.5460.7111-0.3117-0.1877-0.6645-0.96150.6315-0.02490.2113-0.09350.04640.3677-0.0410.475119.37714.049122.2426
125.55170.61240.18887.13431.57972.33850.2007-0.91850.22691.11250.18860.47930.1816-0.21250.06930.19590.1360.15340.34-0.08350.303610.2052-1.236726.226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 102 )L1 - 102
2X-RAY DIFFRACTION2chain 'L' and (resid 103 through 115 )L103 - 115
3X-RAY DIFFRACTION3chain 'L' and (resid 116 through 213 )L116 - 213
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 17 )H1 - 17
5X-RAY DIFFRACTION5chain 'H' and (resid 18 through 60 )H18 - 60
6X-RAY DIFFRACTION6chain 'H' and (resid 61 through 83 )H61 - 83
7X-RAY DIFFRACTION7chain 'H' and (resid 84 through 97 )H84 - 97
8X-RAY DIFFRACTION8chain 'H' and (resid 98 through 131 )H98 - 131
9X-RAY DIFFRACTION9chain 'H' and (resid 132 through 169 )H132 - 169
10X-RAY DIFFRACTION10chain 'H' and (resid 170 through 187 )H170 - 187
11X-RAY DIFFRACTION11chain 'H' and (resid 188 through 206 )H188 - 206
12X-RAY DIFFRACTION12chain 'H' and (resid 207 through 224 )H207 - 224

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