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- PDB-9b75: Crystal structure of humanized 44H10 Fab Version 17 -

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Basic information

Entry
Database: PDB / ID: 9b75
TitleCrystal structure of humanized 44H10 Fab Version 17
Components
  • h44H10-V17 Antibody, heavy chain
  • h44H10-V17 Antibody, light chain
KeywordsIMMUNE SYSTEM / Antibody / Humanized
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKassardjian, A. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148811 Canada
CitationJournal: Antibodies / Year: 2024
Title: Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework.
Authors: Kassardjian, A. / Ivanochko, D. / Barber, B. / Jetha, A. / Julien, J.P.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
H: h44H10-V17 Antibody, heavy chain
L: h44H10-V17 Antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1323
Polymers47,0702
Non-polymers621
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-25 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.923, 84.844, 64.778
Angle α, β, γ (deg.)90.000, 106.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody h44H10-V17 Antibody, heavy chain


Mass: 23717.873 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 h44H10-V17 Antibody, light chain


Mass: 23351.967 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M potassium nitrate pH 6.9

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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: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 27394 / % possible obs: 97.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1054 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.42 Å / SU ML: 0.2322 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.7421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 1376 5.03 %
Rwork0.1797 25992 -
obs0.1819 27368 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3279 0 4 190 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343361
X-RAY DIFFRACTIONf_angle_d0.66654582
X-RAY DIFFRACTIONf_chiral_restr0.0467537
X-RAY DIFFRACTIONf_plane_restr0.0048574
X-RAY DIFFRACTIONf_dihedral_angle_d11.23421197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.31161190.27812364X-RAY DIFFRACTION89.8
2.02-2.10.27171350.23662582X-RAY DIFFRACTION98.26
2.1-2.20.29481380.22052631X-RAY DIFFRACTION99.32
2.2-2.310.2581430.2242665X-RAY DIFFRACTION99.47
2.31-2.460.30681360.21232611X-RAY DIFFRACTION99.42
2.46-2.650.23471400.20962640X-RAY DIFFRACTION99.43
2.65-2.910.26051390.19942602X-RAY DIFFRACTION99.24
2.91-3.330.25281430.17852628X-RAY DIFFRACTION98.23
3.33-4.20.18651360.15492606X-RAY DIFFRACTION97.93
4.2-35.420.16341470.14122663X-RAY DIFFRACTION98.46
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)
17.865366643761.70204398594-2.699843343982.23930671254-0.4628834901493.887911652380.383517362557-0.2255237392140.2301863395070.446725672996-0.124181455551-0.427226529181-0.06892799205380.254865481693-0.2462455727820.2168018514040.0527473653692-0.003592800091760.184461380069-0.02118763993680.289180165616-1.4292.97613.474
23.37293274957-1.0650740570.2584076444473.781109444490.1931140487294.21061051736-0.2426191115480.2985048737680.233420678194-0.1247726216870.166425422976-0.0656370274997-0.0936856032203-0.1410184080360.06564804624180.182541336418-0.03118760500630.006129090654740.2023893166270.02826306224980.191116332613-1.9224.8471.387
33.497343597380.136333808275-0.1006426912494.81858915339-0.2882435679083.2421813651-0.1871472189390.08560803034630.372989778767-0.2126925791090.106133961225-0.256964090263-0.1244770964240.1234679521440.123390730680.174131002098-0.00881317386031-0.02758748125080.199185954762-0.002842033962930.207621051542-1.5184.8674.828
44.749657999810.605678732488-0.3297901715851.957671039531.930334256912.66087539193-0.1531141086430.358554782917-0.233025311536-0.199484080436-0.111110492956-0.579392679903-0.6291756799020.337835408440.3855648152530.434807757420.003829173804910.0285686877720.2348171002470.0219568880050.4793893949575.8930.4350.546
53.17207631645-1.665755085453.1545805990.874236125711-1.671507432173.17843415728-0.325181897878-0.5656291016680.1546985297620.3817721311220.24054062076-0.111000841776-0.582789747258-0.3932888699360.07269317578180.3672633699970.01017270093070.006112590298180.333985676379-0.00799008481330.263338165688-2.348-10.01828.088
65.6752240592-2.821660048650.5019293915166.97538522088-1.063142270435.80371023517-0.217342011504-0.615559533944-0.4853672537820.1313403216490.373703731877-0.2693969381540.1742464400340.223745947805-0.06576034207570.303887501682-0.0571558203855-0.005851150944890.2624804974740.01992382190270.2698728720298.353-19.68428.707
75.49033553298-1.826669062171.54610806412.66231132236-0.2504711223634.48895927055-0.283630996799-0.01430775630530.386907273738-0.04321657249540.0702665055936-0.132930986519-0.5723558883540.2828669102750.1502366673810.316353249881-0.0830628892517-0.0184587944920.2284034200090.04113755890220.27867143018310.7-13.79427.767
85.13975131991-0.7752914900743.126535283295.06645624317-2.445419354846.4864456916-0.02856990366420.325646387794-0.115676804821-0.01929159793160.01156853420860.3353417767730.1628222880550.140335251060.01134967111550.222526101651-0.001907528610020.005745936328410.230041860258-0.04355324541170.2399850894214.46-18.947-8.239
93.61843145199-1.963862400890.1100586082154.4055757716-0.2600183766253.31782754671-0.056389903880.226961324520.1670017572250.130983720278-0.102402316841-0.282338351238-0.2370228408880.349026029060.1572490108450.203123916015-0.0760164814988-0.005791022355540.215958853940.02241824731350.2078652097958.169-10.028-7.243
101.52924352013-2.043453718813.135274811744.31747008546-5.212551305637.06306311312-0.02897098305340.205380357772-0.270413718734-0.1550180392550.02631111377630.002104006486830.02945906486080.284377418249-0.01862293797760.2364058275950.02450149639130.03137905217140.280951726801-0.01333209991660.25232447225412.136-28.1156.05
112.93038358509-0.767027002981-2.573337091130.6735447317480.8816486016786.964441554140.152940951361-0.0293461751294-0.0321576806829-0.03386129879520.0446275637385-0.0376834856821-0.327788150072-0.035891486635-0.2056236360490.204893773176-0.0107107073382-0.04054165165030.2232699449130.03315910566460.2596165097885.016-27.65424.254
121.7394987544-0.950916745107-2.054261242362.489983490191.529549540215.9003793296-0.17616580023-0.169902405248-0.143755709460.2617096333810.1565359699910.1886323416090.481742547097-0.0495316406940.02575638571620.205711628166-0.0350185703657-0.01240082300430.2991854730950.04371054401380.2514121805652.978-33.51730.913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:17 )H1 - 17
2X-RAY DIFFRACTION2( CHAIN H AND RESID 18:71 )H18 - 71
3X-RAY DIFFRACTION3( CHAIN H AND RESID 72:99 )H72 - 99
4X-RAY DIFFRACTION4( CHAIN H AND RESID 100:109 )H100 - 109
5X-RAY DIFFRACTION5( CHAIN H AND RESID 110:125 )H110 - 125
6X-RAY DIFFRACTION6( CHAIN H AND RESID 126:149 )H126 - 149
7X-RAY DIFFRACTION7( CHAIN H AND RESID 150:214 )H150 - 214
8X-RAY DIFFRACTION8( CHAIN L AND RESID 1:25 )L1 - 25
9X-RAY DIFFRACTION9( CHAIN L AND RESID 26:101 )L26 - 101
10X-RAY DIFFRACTION10( CHAIN L AND RESID 102:113 )L102 - 113
11X-RAY DIFFRACTION11( CHAIN L AND RESID 114:174 )L114 - 174
12X-RAY DIFFRACTION12( CHAIN L AND RESID 175:212 )L175 - 212

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