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- PDB-6ss5: Structure of the arginase-2-inhibitory human antigen-binding frag... -

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Basic information

Entry
Database: PDB / ID: 6ss5
TitleStructure of the arginase-2-inhibitory human antigen-binding fragment Fab C0020187
Components(Fab C0020187 ...) x 2
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBurschowsky, D. / Addyman, A. / Fiedler, S. / Groves, M. / Haynes, S. / Seewooruthun, C. / Carr, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC1362/A20263 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation.
Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Chan, D.T.Y. / Jenkinson, L. / Haynes, S.W. / Austin, M. / Diamandakis, A. / Burschowsky, D. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Gowans, E. / Shibata, Y. / Barnard, M. / Wilkinson, R.W. / Vaughan, T.J. / Holt, S.V. / Cerundolo, V. / Carr, M.D. / Groves, M.A.T.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 1.4Nov 20, 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
HHH: Fab C0020187 heavy chain (IgG1)
LLL: Fab C0020187 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,64813
Polymers47,5442
Non-polymers1,10411
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-112 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 103.370, 164.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11LLL-572-

HOH

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Components

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Antibody , 2 types, 2 molecules HHHLLL

#1: Antibody Fab C0020187 heavy chain (IgG1)


Mass: 24479.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Amino acids are numbered according to the Kabat numbering scheme.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO
Production host: Cricetinae gen. sp.Cricetulus griseus (Chinese hamster)
Variant (production host): ExpiCHO
#2: Antibody Fab C0020187 light chain (IgG1)


Mass: 23064.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we ...Details: Amino acids are numbered according to the Kabat numbering scheme. Residue 10 would not be present in the Kabat scheme, but due to problems with non-continuous numbering in L-peptides, we included it. Therefore, residues 2-10 should be read as 1-9, per Kabat.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEU1.3 fab / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): ExpiCHO

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Non-polymers , 5 types, 329 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.19 Å3/Da / Density % sol: 61.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5 70% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.78→49.355 Å / Num. obs: 58306 / % possible obs: 99.7 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.1
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 8.5 % / Rmerge(I) obs: 4.11 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3268 / CC1/2: 0.31 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRV

6srv


Resolution: 1.78→49.354 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.725 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2165 2923 5.017 %
Rwork0.1781 --
all0.18 --
obs-58262 99.598 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.211 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2--3.811 Å20 Å2
3----1.421 Å2
Refinement stepCycle: LAST / Resolution: 1.78→49.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 64 318 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173149
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.6564810
X-RAY DIFFRACTIONr_angle_other_deg1.4511.5857374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.1515.445483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66223.047128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26215524
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.578152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2951511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02683
X-RAY DIFFRACTIONr_nbd_refined0.1940.2578
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22967
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21651
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2960.2309
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.212
X-RAY DIFFRACTIONr_nbd_other0.2520.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.218
X-RAY DIFFRACTIONr_mcbond_it2.9023.2331829
X-RAY DIFFRACTIONr_mcbond_other2.8993.2331828
X-RAY DIFFRACTIONr_mcangle_it3.9674.8312302
X-RAY DIFFRACTIONr_mcangle_other3.9674.8322303
X-RAY DIFFRACTIONr_scbond_it4.2963.7341685
X-RAY DIFFRACTIONr_scbond_other4.2833.7341682
X-RAY DIFFRACTIONr_scangle_it6.3515.3912508
X-RAY DIFFRACTIONr_scangle_other6.3365.392503
X-RAY DIFFRACTIONr_lrange_it7.99739.8243830
X-RAY DIFFRACTIONr_lrange_other7.99639.843831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.8260.372130.3784027X-RAY DIFFRACTION99.1349
1.826-1.8760.3522140.3433917X-RAY DIFFRACTION98.9698
1.876-1.930.3321900.3123802X-RAY DIFFRACTION99.2788
1.93-1.990.2781990.2783739X-RAY DIFFRACTION99.2189
1.99-2.0550.2861700.2543622X-RAY DIFFRACTION99.7632
2.055-2.1270.2511620.2273508X-RAY DIFFRACTION99.5389
2.127-2.2070.2431840.213395X-RAY DIFFRACTION99.6381
2.207-2.2970.2241670.1853280X-RAY DIFFRACTION99.7107
2.297-2.3990.2371690.1783114X-RAY DIFFRACTION99.7872
2.399-2.5160.2241690.183016X-RAY DIFFRACTION99.8433
2.516-2.6510.1911420.1612863X-RAY DIFFRACTION99.8339
2.651-2.8120.1951670.1552678X-RAY DIFFRACTION99.8947
2.812-3.0050.2281550.1532549X-RAY DIFFRACTION99.963
3.005-3.2450.191260.1562387X-RAY DIFFRACTION99.9602
3.245-3.5530.1951190.1482194X-RAY DIFFRACTION100
3.553-3.970.184930.1422031X-RAY DIFFRACTION99.7651
3.97-4.5790.173950.1221767X-RAY DIFFRACTION99.8391
4.579-5.5960.179730.141537X-RAY DIFFRACTION100
5.596-7.8640.204730.1751199X-RAY DIFFRACTION100
7.864-49.3540.188430.159714X-RAY DIFFRACTION100

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