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- PDB-8t7g: Structure of the CK variant of Fab F1 (FabC-F1) -

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Basic information

Entry
Database: PDB / ID: 8t7g
TitleStructure of the CK variant of Fab F1 (FabC-F1)
Components(CK variant of Fab F1 ...) x 2
KeywordsIMMUNE SYSTEM / enhanced crystallization / EphA2 binding / engineered protein / Fab
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSinger, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
Funding support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S.
#1: Journal: J.Mol.Biol. / Year: 2018
Title: Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.
Authors: Bailey, L.J. / Sheehy, K.M. / Dominik, P.K. / Liang, W.G. / Rui, H. / Clark, M. / Jaskolowski, M. / Kim, Y. / Deneka, D. / Tang, W.J. / Kossiakoff, A.A.
#2: Journal: Plos One / Year: 2020
Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
History
DepositionJun 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 6, 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
A: CK variant of Fab F1 heavy chain
B: CK variant of Fab F1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04311
Polymers48,6002
Non-polymers4439
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-74 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.707, 73.752, 70.029
Angle α, β, γ (deg.)90.000, 116.540, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody CK variant of Fab F1 heavy chain


Mass: 25332.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab selected/engineered by phage display / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody CK variant of Fab F1 light chain


Mass: 23267.811 Da / Num. of mol.: 1 / Mutation: HAGLSSP replaced by QGTTS
Source method: isolated from a genetically manipulated source
Details: Fab selected/engineered by phage display / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 222 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 22% PEG8000, 200 mM sodium chloride, 100 mM sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→62.65 Å / Num. obs: 40653 / % possible obs: 96.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.058 / Rrim(I) all: 0.12 / Net I/σ(I): 12.7
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1987 / CC1/2: 0.373 / Rpim(I) all: 0.87 / % possible all: 78.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSAUTOPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8T7F

8t7f


Resolution: 2→62.65 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 1703 5.25 %
Rwork0.1944 30735 -
obs0.1962 32438 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.17 Å2
Refinement stepCycle: LAST / Resolution: 2→62.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 21 213 3367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683240
X-RAY DIFFRACTIONf_angle_d0.85714412
X-RAY DIFFRACTIONf_chiral_restr0.0566507
X-RAY DIFFRACTIONf_plane_restr0.0172563
X-RAY DIFFRACTIONf_dihedral_angle_d15.42071129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.30251490.25542545X-RAY DIFFRACTION99.34
2.06-2.130.36231400.26842529X-RAY DIFFRACTION97.84
2.13-2.20.3141480.25322562X-RAY DIFFRACTION99.27
2.2-2.290.31021360.29662426X-RAY DIFFRACTION94.33
2.29-2.390.26091560.21542580X-RAY DIFFRACTION99.24
2.39-2.520.26821430.21452534X-RAY DIFFRACTION98.49
2.52-2.680.27251090.22222628X-RAY DIFFRACTION99.42
2.68-2.880.26831260.21812587X-RAY DIFFRACTION99.67
2.88-3.170.25241360.20462609X-RAY DIFFRACTION99.2
3.17-3.630.19671420.18942548X-RAY DIFFRACTION97.85
3.63-4.580.17941600.15242559X-RAY DIFFRACTION98.8
4.58-62.650.19521580.15812628X-RAY DIFFRACTION98.65
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)
15.40638876034-2.1229572426-0.2497983050853.55369132874-2.922023488043.44586732631-0.09144641006770.1367697230230.428223563462-0.0158257564860.8276076685810.28839109656-0.5811656643510.425135770771-0.4822776497020.4071917064010.0109844532670.06508903202090.449954002294-0.240703079950.2753516876838.066457894712.0216723267916.5996923127
23.26596993772-0.2993098838550.3001250923464.9758279347-1.04087248073.41705250931-0.491289518652-1.033391630280.1914845767810.260030999460.6092659623010.544584849389-0.277303374874-0.613845691255-0.1478806638860.2972549568020.07726219925570.03437022408360.583815781760.03791167524520.318646433058-0.215595574993-1.7691134925822.0840846038
32.34301702364-0.5822968996650.6331701358684.33885843051-0.9305849289232.35154929177-0.378299541116-1.381250208740.4125552996150.5927159043670.4968379521730.359160279174-0.496732295408-0.200296752765-0.1049787386720.5347480372640.1326324474950.009545848595850.821260399385-0.2547294465450.4280856473423.176636600044.9586510266726.5283441161
45.76884242248-0.6841757495550.8557740457875.528340430180.8834950446582.85869600508-0.407004272416-0.904784059164-0.200036804327-0.0795246243110.5677756845560.802326716831-0.386616773502-0.383160625391-0.1294813134860.306830908070.0591921437070.02251018652120.5312107607890.1612439450960.304677361517-1.73370087358-5.8374417136119.1269831536
52.49907050035-0.01597055370930.1670936937340.3076390322330.06344706747322.77785824565-0.0300760221389-1.038041510170.765251383309-0.04602962386940.170652023184-0.29185016407-0.3462784978930.365801741594-0.1659154055050.422804403296-0.0647184403567-0.04149025553910.398618226047-0.1538267750130.38680833403821.5677456631-0.37011417745315.9278422619
66.297906116441.526343846470.1551096399085.41599204766-0.7266695520692.706794918630.07981453648790.352110059157-0.292441778087-0.4608650493070.1435314518690.09187217534010.179899131480.250032722542-0.2201996180870.2277428551470.0327413136291-0.04915309427740.148491829332-0.006435190565090.20564148703826.3725599709-15.6210496566-0.865285177133
74.50238306081.335839764030.5475830611317.052537209952.7441278455.91042228810.1760392998-0.0459666378365-0.178320833502-0.04626731716650.03729502823770.1441012299960.178799655788-0.0826515000047-0.1922553906140.185883892006-0.00595549328375-0.006892778331310.1303948343440.02168306023120.2176652023620.0041177086-13.82820016443.19880592012
85.03472410271.02631389740.05948171264228.391316699083.518749302116.726268152370.01816154330420.3711438750450.0517881479845-1.087876360020.122153507010.365725091834-0.56717658665-0.11852184773-0.1615531813710.32738973921-0.00692112152119-0.04009250810770.1649559290870.0524326037720.25591770658919.4538715732-8.52348676954-3.96326619817
96.09689769813-1.89142930904-0.5667967744522.096012458975.187963174169.252519201810.2714323017270.4489359991620.0967036953851-0.613172080846-0.3721116001670.274697563917-0.2507224823860.2641698974330.1376686174250.4256375877130.02343899719990.06246938280470.2265358145120.07140244584750.24142069384724.2585385891-7.34839793468-5.26608519487
103.86879793353-0.0143710289408-0.9743957747073.04369404839-1.182437616691.25906001715-0.0699662621881-1.31881373178-0.6180588600650.611457600270.3053106106630.3953943447330.116360363275-0.133328460854-0.2308817415550.421177571807-0.00791365545914-0.01447377286510.8809469404550.4448484442730.576114310188-0.879305321493-23.167397845827.099712732
110.4304942814750.202407968237-0.3132950805762.872086072690.04810821481810.5232587004390.1041269110670.0218089430233-0.419468596379-0.4802855166740.2735993803720.4453975677730.015625201267-0.986098866177-0.3291141993450.292539043839-0.0476256998844-0.1167749839740.863356075690.5106790110710.802510064292-6.66785056849-18.063426364917.2609066416
123.069426289571.583972887710.2194048077023.164449139580.005211472655791.090588307590.00477251965031-0.65877908703-0.7079821670650.1493016123740.2090169688890.5024794957570.190641593032-0.569002739105-0.2122807555210.303424272811-0.0915415989068-0.09907504600970.7554341997820.4131113128250.733177090059-3.39983496168-24.108076989222.4600432789
134.557680906112.20775017626-0.780911785741.58842614981-1.102035825721.134969854350.158482440699-1.120243228570.476438892220.5838033044910.4331136434950.62378826318-0.452533175692-0.808452550512-0.5238604519180.4884442426050.1602657260410.150112407051.198345422840.2759355885730.467554579492-2.52766901276-11.353582752830.9665661652
144.20886843784-2.85339227836-3.615704266511.907689236712.450134880893.14768393191-0.446713516951-0.377283485289-0.9724427432940.2984631918850.3145630483320.5366646558610.542795978841-0.114675890150.140761009260.412491217985-0.0486873852883-0.02370319238740.3737144617410.2237506106110.66659451578210.5864503798-32.237752656312.215076371
154.853194773510.593366166172-1.23956994179.05616304326-2.80735819276.263907469110.295847603304-0.1520072896610.5381962371-0.624677242444-0.492248877302-0.17782997254-0.1300262733870.4329336051230.1386045673760.2127026782180.0186892574886-0.006453118415750.1737150935070.000913998336760.31037684435933.5476191144-17.2816792229-0.64098675429
169.011257169372.08247426528-1.080493581136.07139623687-1.771513582824.37244054154-0.0427396528504-0.465720688786-0.194498739490.02588436929070.03856395019220.1968725780220.263871878047-0.071713384543-0.03819715228860.2541143074910.00727414698797-0.02374384995490.128884815191-0.01118657194650.21498465119926.6624366083-27.14765560897.89558218344
178.22668015675-3.10593403153-2.331349729215.08764728702-0.1758581537563.68510670653-0.299736648158-0.501316061271-0.03756065772530.5383321126590.291673262301-0.227570717859-0.1356597626120.6416889202690.02094406826950.293614894491-0.0349279739729-0.08199412722850.303840115459-0.001186352046510.27659813980634.6129959286-24.816811173411.8828366391
182.019482791333.001208253710.02975171746317.3706642945-0.8386069607925.51727295330.173078837335-0.01787608753180.464825121449-0.009047345367950.3047415437991.208052223350.141405324662-1.081191515-0.4876570522470.328916516945-0.0756654647914-0.002087242268960.3938436024890.149824973970.66699671001111.3771149754-26.19913952998.02708806958
192.036062680142.31254753835-2.029464569146.649764419-0.8894618466265.635768271930.28608745892-0.4240075883170.5346078024580.227340544053-0.0225301437947-0.833226802865-0.1763977301090.82015792648-0.1758417986710.241851868478-0.0193856222677-0.03057738784420.246776400219-0.01806813028490.41185909802138.6180576603-18.69429431926.11858680408
209.256126864074.474856905-3.237774571048.46630309002-2.732635755624.77094447101-0.2529632154550.0381381027429-0.000931195458365-0.523542093990.0215304644694-0.2998435777060.3873607259430.1166982581720.2231757382710.2948706955030.04915118975150.002550092696910.1515211059440.006005297614730.30440569907934.6885939452-30.59989128352.8941409874
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 18 )AA1 - 181 - 17
22chain 'A' and (resid 19 through 57 )AA19 - 5718 - 52
33chain 'A' and (resid 58 through 99 )AA58 - 9953 - 91
44chain 'A' and (resid 100 through 130 )AA100 - 13092 - 110
55chain 'A' and (resid 131 through 143 )AA131 - 143111 - 123
66chain 'A' and (resid 144 through 169 )AA144 - 169124 - 144
77chain 'A' and (resid 170 through 212 )AA170 - 212145 - 187
88chain 'A' and (resid 213 through 227 )AA213 - 227188 - 202
99chain 'A' and (resid 228 through 238 )AA228 - 238203 - 213
1010chain 'B' and (resid 1 through 44 )BC1 - 441 - 38
1111chain 'B' and (resid 45 through 75 )BC45 - 7539 - 61
1212chain 'B' and (resid 76 through 106 )BC76 - 10662 - 90
1313chain 'B' and (resid 107 through 119 )BC107 - 11991 - 101
1414chain 'B' and (resid 120 through 131 )BC120 - 131102 - 113
1515chain 'B' and (resid 132 through 146 )BC132 - 146114 - 128
1616chain 'B' and (resid 147 through 168 )BC147 - 168129 - 150
1717chain 'B' and (resid 169 through 181 )BC169 - 181151 - 163
1818chain 'B' and (resid 182 through 192 )BC182 - 192164 - 174
1919chain 'B' and (resid 193 through 206 )BC193 - 206175 - 188
2020chain 'B' and (resid 207 through 231 )BC207 - 231189 - 211

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