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- PDB-6ss0: Structure of the arginase-2-inhibitory human antigen-binding frag... -

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Basic information

Entry
Database: PDB / ID: 6ss0
TitleStructure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021181
Components(Fab C0021181 ...) x 2
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SUCCINIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Mabs
Title: Structural and functional characterization of C0021158, a high-affinity monoclonal antibody that inhibits Arginase 2 function via a novel non-competitive mechanism of action.
Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / ...Authors: Austin, M. / Burschowsky, D. / Chan, D.T.Y. / Jenkinson, L. / Haynes, S. / Diamandakis, A. / Seewooruthun, C. / Addyman, A. / Fiedler, S. / Ryman, S. / Whitehouse, J. / Slater, L.H. / Hadjinicolaou, A.V. / Gileadi, U. / Gowans, E. / Shibata, Y. / Barnard, M. / Kaserer, T. / Sharma, P. / Luheshi, N.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 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 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 1.3Oct 9, 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
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
III: Fab C0021181 heavy chain (IgG1)
MMM: Fab C0021181 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,73514
Polymers95,8894
Non-polymers84710
Water10,377576
1
HHH: Fab C0021181 heavy chain (IgG1)
LLL: Fab C0021181 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2757
Polymers47,9442
Non-polymers3315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-31 kcal/mol
Surface area19420 Å2
MethodPISA
2
III: Fab C0021181 heavy chain (IgG1)
MMM: Fab C0021181 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4607
Polymers47,9442
Non-polymers5165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 67.370, 94.330
Angle α, β, γ (deg.)90.000, 100.239, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains H I
22Chains L M
/ NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 4 molecules HHHIIILLLMMM

#1: Antibody Fab C0021181 heavy chain (IgG1)


Mass: 24819.836 Da / Num. of mol.: 2
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: Cricetulus griseus (Chinese hamster) / Strain (production host): ExpiCHO
#2: Antibody Fab C0021181 light chain (IgG1)


Mass: 23124.482 Da / Num. of mol.: 2
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) / Strain (production host): ExpiCHO

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Non-polymers , 5 types, 586 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM SPG pH 7.0 25% PEG1500 PACT A4 SPG: succinic acid, phosphate, glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.7→46.548 Å / Num. obs: 88773 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4541 / CC1/2: 0.36 / % possible all: 99.9

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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: 1.7→46.544 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.339 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2242 4494 5.062 %
Rwork0.1894 --
all0.191 --
obs-88772 99.918 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.241 Å2
Baniso -1Baniso -2Baniso -3
1--1.397 Å20 Å2-0.389 Å2
2---0.234 Å20 Å2
3---1.662 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 0 51 576 7042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176037
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6439174
X-RAY DIFFRACTIONr_angle_other_deg1.2221.56814095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2822.06267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.464151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4011531
X-RAY DIFFRACTIONr_chiral_restr0.0520.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021363
X-RAY DIFFRACTIONr_nbd_refined0.1780.2927
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.25422
X-RAY DIFFRACTIONr_nbtor_refined0.1530.23120
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2437
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.241
X-RAY DIFFRACTIONr_nbd_other0.2110.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.241
X-RAY DIFFRACTIONr_mcbond_it1.3752.693500
X-RAY DIFFRACTIONr_mcbond_other1.3742.693499
X-RAY DIFFRACTIONr_mcangle_it2.2384.0224389
X-RAY DIFFRACTIONr_mcangle_other2.2374.0224390
X-RAY DIFFRACTIONr_scbond_it1.6572.8763221
X-RAY DIFFRACTIONr_scbond_other1.6572.8773222
X-RAY DIFFRACTIONr_scangle_it2.6634.2074785
X-RAY DIFFRACTIONr_scangle_other2.6634.2084786
X-RAY DIFFRACTIONr_lrange_it4.50631.4177028
X-RAY DIFFRACTIONr_lrange_other4.50531.4257029
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.056486
X-RAY DIFFRACTIONr_ncsr_local_group_20.0680.056279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.3373150.34161970.34165200.6230.60699.87730.343
1.744-1.7920.3253550.31359850.31463450.7080.71299.92120.313
1.792-1.8440.2923250.28258750.28262010.7780.79799.98390.279
1.844-1.90.2943280.26956720.27160050.8120.82199.91670.263
1.9-1.9630.2723080.23555510.23758590.8570.8741000.227
1.963-2.0310.2792880.21953540.22256440.870.89599.96460.21
2.031-2.1080.2342860.20151910.20354790.9120.92299.96350.192
2.108-2.1940.2472580.18949520.19252120.9060.92999.96160.181
2.194-2.2910.2152590.18947700.1950290.9270.9361000.183
2.291-2.4030.2492120.18646190.18948320.9180.93799.97930.182
2.403-2.5320.2152230.18743690.18845930.9280.94299.97820.186
2.532-2.6850.2321990.1941250.19243260.9320.94399.95380.194
2.685-2.870.231810.18638930.18840760.9320.94399.95090.196
2.87-3.0990.2131880.18636260.18738170.9410.94999.92140.202
3.099-3.3930.2071880.1833200.18135120.9510.95299.88610.201
3.393-3.7910.1991480.16930350.1731840.9530.9699.96860.194
3.791-4.3730.1851450.14926710.15128200.9630.96999.85820.182
4.373-5.3440.1861150.13922680.14123880.9650.97499.79060.179
5.344-7.5080.2081160.15917700.16218880.960.96799.89410.2
7.508-46.5440.177570.18210350.18110930.9620.96499.90850.248

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