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- PDB-6z3x: Crystal structure of the designed antibody DesAb-anti-HSA-P1 -

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Basic information

Entry
Database: PDB / ID: 6z3x
TitleCrystal structure of the designed antibody DesAb-anti-HSA-P1
ComponentsDesAb-anti-HSA-P1
KeywordsIMMUNE SYSTEM / protein design / artificial antibody / specific interaction
Function / homologyCACODYLATE ION / IMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsCostanzi, E. / Sormanni, P. / Ricagno, S.
CitationJournal: Sci Adv / Year: 2022
Title: Fragment-based computational design of antibodies targeting structured epitopes.
Authors: Aguilar Rangel, M. / Bedwell, A. / Costanzi, E. / Taylor, R.J. / Russo, R. / Bernardes, G.J.L. / Ricagno, S. / Frydman, J. / Vendruscolo, M. / Sormanni, P.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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

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Assembly

Deposited unit
A: DesAb-anti-HSA-P1
B: DesAb-anti-HSA-P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,98110
Polymers30,0672
Non-polymers9148
Water2,450136
1
A: DesAb-anti-HSA-P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1702
Polymers15,0341
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DesAb-anti-HSA-P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8118
Polymers15,0341
Non-polymers7777
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.718, 52.411, 99.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULEULEU(chain 'A' and (resid 2 through 21 or resid 23...AA2 - 212 - 21
12CYSCYSPHEPHE(chain 'A' and (resid 2 through 21 or resid 23...AA23 - 2823 - 28
13ILEILEGLNGLN(chain 'A' and (resid 2 through 21 or resid 23...AA30 - 4030 - 40
14LYSLYSTYRTYR(chain 'A' and (resid 2 through 21 or resid 23...AA44 - 9644 - 96
15ALAALAILEILE(chain 'A' and (resid 2 through 21 or resid 23...AA98 - 10298 - 102
16LEULEUSERSER(chain 'A' and (resid 2 through 21 or resid 23...AA113 - 128113 - 128
27GLUGLULEULEU(chain 'B' and (resid 2 through 21 or resid 23...BB2 - 212 - 21
28CYSCYSPHEPHE(chain 'B' and (resid 2 through 21 or resid 23...BB23 - 2823 - 28
29ILEILEGLNGLN(chain 'B' and (resid 2 through 21 or resid 23...BB30 - 4030 - 40
210LYSLYSTYRTYR(chain 'B' and (resid 2 through 21 or resid 23...BB44 - 9644 - 96
211ALAALAILEILE(chain 'B' and (resid 2 through 21 or resid 23...BB98 - 10298 - 102
212LEULEUSERSER(chain 'B' and (resid 2 through 21 or resid 23...BB113 - 128113 - 128

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Components

#1: Antibody DesAb-anti-HSA-P1


Mass: 15033.509 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium cacodylate ph 6.5, 27% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→46.34 Å / Num. obs: 45160 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.7
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 0.776 / Num. unique obs: 2432 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9V

3b9v


Resolution: 1.74→46.34 Å / SU ML: 0.2058 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 2104 5.01 %
Rwork0.1925 39898 -
obs0.1939 42002 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.82 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 36 136 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951938
X-RAY DIFFRACTIONf_angle_d1.04892639
X-RAY DIFFRACTIONf_chiral_restr0.5452286
X-RAY DIFFRACTIONf_plane_restr0.007338
X-RAY DIFFRACTIONf_dihedral_angle_d16.3278672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.32761080.33782736X-RAY DIFFRACTION99.75
1.78-1.830.32511210.3212640X-RAY DIFFRACTION99.53
1.83-1.870.31471380.27512683X-RAY DIFFRACTION99.86
1.87-1.930.32121550.23822636X-RAY DIFFRACTION99.54
1.93-1.990.20651470.20872622X-RAY DIFFRACTION99.75
1.99-2.060.24731370.19892683X-RAY DIFFRACTION99.65
2.06-2.150.22741670.19712642X-RAY DIFFRACTION100
2.15-2.240.25671260.18952663X-RAY DIFFRACTION99.96
2.24-2.360.23441490.1952654X-RAY DIFFRACTION99.93
2.36-2.510.21531510.18282653X-RAY DIFFRACTION99.93
2.51-2.70.24251450.19162657X-RAY DIFFRACTION99.93
2.7-2.970.2161300.16952660X-RAY DIFFRACTION99.82
2.98-3.410.16581450.1662671X-RAY DIFFRACTION100
3.41-4.290.19891670.15642630X-RAY DIFFRACTION100
4.29-46.340.2061180.1982668X-RAY DIFFRACTION99.22
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)
11.812167942351.37893088269-0.4363298584441.698391838710.1466956946670.848747957892-0.1433367099010.326525055077-0.109872998622-0.1955018006720.202689866399-0.03886626212280.0263045737279-0.00747469769315-0.0325369720030.199545393185-0.00969356526260.0005616913322950.246926165922-0.02444060520890.230737072523-14.18842700597.15928141536-42.654772207
23.798242984010.8562517292140.2767003047271.429670161860.2309135932311.40463418288-0.01305766855980.13745202290.118562307408-0.0301957619373-0.02302989660390.0952392073174-0.151343876947-0.02123477448940.02670922005490.2022829373520.0178927305509-0.01183950090640.1928001017260.005623707250420.175266407798-14.263752333812.9727960818-34.0702237802
30.00591260986193-0.007294778777520.003066113739850.00822063092160.003856398835780.0681070763241-0.043089688383-0.06503069385660.13650557687-0.0204086730515-0.0714195599557-0.118733822919-0.1392954050620.0631645543575-2.15767570478E-61.501941062030.167496324244-0.379739152330.709965859727-0.1014518405540.736091681388.1156331081911.7369591933-25.3060057355
41.902435263861.66976607143-1.07545358712.96260622349-0.1894256282883.18144359222-0.4162357635850.888571450103-0.860142343939-0.2265482138920.359521461571-0.5180249752310.02232392440970.9229291962460.1606016986220.295291168351-0.03204701143740.02852761183260.501077711391-0.07945449809090.3141614377423.303853410783.87628866759-19.6671438196
52.70341197841-1.01554115802-2.50046766753.177749098021.411926623448.223262809650.179433514718-0.398562088671-0.307418197634-0.2191651044570.153165670630.196712083198-0.00758405826831-1.15350086637-0.1743183817190.188562753343-0.0430152970272-0.01711669490070.3225753727380.01332375271520.303654208735-19.87165785966.9365606701-15.4948793758
62.15083622027-2.139550151610.5249314832852.63855855130.4068938597921.75779288465-0.0624204037714-0.0237350803493-0.502337559512-0.06740838819180.1642453882580.1127166699990.1994949917120.253621943815-0.01305447721760.2195528774620.01009673446110.01384071304030.190694524074-0.005380345681050.203501303723-0.5897732280132.78144601597-13.1629387264
75.40616267058-2.63141677892.871945098183.52060896016-1.140188082562.77571056503-0.02069512945810.2712241890770.0227887328710.1890801654610.00872709379589-0.133112679173-0.163505654930.4173031171270.04078642839070.218844653222-0.0195201860932-0.02088430557280.265246455394-0.002078670628850.2064781193691.3851100718310.4902888956-10.7152239654
82.08789239037-0.4583179074742.90959873832.47599496325-1.957113067536.988994403430.03965790038060.1879397671490.0434966222665-0.1012481948960.08554255520060.604993535257-0.5936911824440.32111886174-0.001648758204170.293170197889-0.0107287906817-0.05330722290410.2053596706680.006272441925430.28183625485-5.5928957256517.6596938881-13.8476561377
97.8294825086-4.68682529382.086297797333.19142334058-0.7417086182611.38753792065-0.3537778341770.03837036379850.08332201896340.5468553438950.183946963342-0.168308477163-0.0875197333144-0.06466670407540.1462604959990.2536713865840.00149984767704-0.03242155075880.3017691708180.0275190580390.217258690780.79808751674210.6477426653-0.81862404944
102.02139975032-1.7478676804-0.5010873652843.54522127443-0.03111660105141.21990658483-0.0973701083562-0.148376787153-0.1765513189940.5098840319580.1315581704820.06136108616550.037058244722-0.0318563648751-0.006539644512480.263944744120.03582537982010.008178555149920.2372202295780.008797668493070.225898716133-6.643345359668.71341491496-5.2669246605
112.77352879005-0.9626896263780.1702527476871.25059600862-0.1110129720752.232373948780.029479719683-0.147640513504-0.2123413826860.112448719003-0.03399889899820.0649034244545-0.142022611416-0.00917626997970.05895667152530.197710651651-0.0139716453574-0.006053336756460.167614020275-0.0152742704040.158953229811-8.2027461409710.1992435246-12.7447259103
120.356428779567-0.2215008086110.4337875449770.891051567975-0.05333020808550.9645987268570.0985447210419-0.5106410332230.3630311396960.11989030449-0.0601043272906-0.0881684677116-0.4696866007790.244870729531-0.0385372652580.299191276197-0.0726981081535-0.00436895393460.439198600866-0.04054661211680.25405241633-0.98003176727413.6885468933-16.0884132514
132.192567131151.2588442827-1.941659988290.796371791713-0.854988606412.657201826290.0672847157393-0.745293728349-0.4931816156810.352197579955-0.2311034167350.525764394960.183218236027-0.1746913212470.2654992962210.296202118904-0.02316505746840.00137675863260.342993165254-0.04661111092660.348194168065-24.9781498275.13230626318-29.1122467837
144.441073762510.07582406950360.4984147545160.781264581051-0.2711042388631.22924748659-0.003516151375950.389365389904-0.2354953705170.07838974826960.03720361050540.03571704773970.1024121291890.024700977107-0.03395671147790.1970707651850.0136119953312-0.02096557461980.218083772428-0.0277284393310.233920603151-15.99903525424.61780927383-36.4655111975
152.288115240750.7081562132290.05431254097983.099136067910.6998115226792.451634166730.0599662219540.1335712355520.2366443762180.3421357854640.0102908114341-0.131202948064-0.3072586976570.0538963479452-0.1056302624370.27025552280.0143943230378-0.04467688344760.2188886522540.0007255268322610.26367764155-14.18092934916.1356867281-33.8480905421
166.978503819243.618332328555.836523031774.381993464963.191596380944.97528255827-0.1599113847950.3866519978870.0985967736693-0.2123556433960.08706132158420.0585954841824-0.3277021023530.06226045608340.2088771304880.2157088581060.010143212859-0.006370597498860.2797825767760.03200367000050.167759143572-18.815305222913.5622862287-44.7527874151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 62 through 84 )
2X-RAY DIFFRACTION2chain 'B' and (resid 85 through 128 )
3X-RAY DIFFRACTION3chain 'B' and (resid 129 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 8 )
5X-RAY DIFFRACTION5chain 'A' and (resid 9 through 18 )
6X-RAY DIFFRACTION6chain 'A' and (resid 19 through 29 )
7X-RAY DIFFRACTION7chain 'A' and (resid 30 through 40 )
8X-RAY DIFFRACTION8chain 'A' and (resid 41 through 53 )
9X-RAY DIFFRACTION9chain 'A' and (resid 54 through 61 )
10X-RAY DIFFRACTION10chain 'A' and (resid 62 through 77 )
11X-RAY DIFFRACTION11chain 'A' and (resid 78 through 101 )
12X-RAY DIFFRACTION12chain 'A' and (resid 102 through 128 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 8 )
14X-RAY DIFFRACTION14chain 'B' and (resid 9 through 33 )
15X-RAY DIFFRACTION15chain 'B' and (resid 34 through 45 )
16X-RAY DIFFRACTION16chain 'B' and (resid 46 through 61 )

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