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

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Basic information

Entry
Database: PDB / ID: 6srv
TitleStructure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021144
Components(Fab C0021144 ...) x 2
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 C0021144 heavy chain (IgG1)
III: Fab C0021144 heavy chain (IgG1)
LLL: Fab C0021144 light chain (IgG1)
MMM: Fab C0021144 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42730
Polymers95,4324
Non-polymers1,99426
Water1,40578
1
HHH: Fab C0021144 heavy chain (IgG1)
LLL: Fab C0021144 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,88917
Polymers47,7162
Non-polymers1,17315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-9 kcal/mol
Surface area20490 Å2
MethodPISA
2
III: Fab C0021144 heavy chain (IgG1)
MMM: Fab C0021144 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53813
Polymers47,7162
Non-polymers82211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-14 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.690, 172.690, 211.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11HHH-301-

CL

21HHH-311-

PEG

31III-301-

CL

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Components

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Antibody , 2 types, 4 molecules HHHIIILLLMMM

#1: Antibody Fab C0021144 heavy chain (IgG1)


Mass: 24688.682 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 C0021144 light chain (IgG1)


Mass: 23027.447 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, 104 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM NH4Cl 20% PEG3350

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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 PILATUS 6M-F / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→49.901 Å / Num. obs: 47369 / % possible obs: 100 % / Redundancy: 29.5 % / CC1/2: 1 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.066 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 20.9 % / Rmerge(I) obs: 9.9 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4600 / CC1/2: 0.35 / Rpim(I) all: 2.226 / Rrim(I) all: 10.19 / % 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 / Resolution: 2.4→49.901 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 26.953 / SU ML: 0.257 / Cross valid method: FREE R-VALUE / ESU R: 0.304 / ESU R Free: 0.227
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2413 2368 4.999 %
Rwork0.2051 --
all0.207 --
obs-47369 99.924 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.969 Å2
Baniso -1Baniso -2Baniso -3
1--1.011 Å2-0.506 Å20 Å2
2---1.011 Å20 Å2
3---3.281 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6489 0 126 78 6693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176127
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6459166
X-RAY DIFFRACTIONr_angle_other_deg1.2321.56914290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7625870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57422.812256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3031524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021314
X-RAY DIFFRACTIONr_nbd_refined0.1870.21026
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25284
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23090
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2149
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.216
X-RAY DIFFRACTIONr_nbd_other0.1810.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.26
X-RAY DIFFRACTIONr_mcbond_it2.2783.8453496
X-RAY DIFFRACTIONr_mcbond_other2.2623.8373491
X-RAY DIFFRACTIONr_mcangle_it3.6925.7454358
X-RAY DIFFRACTIONr_mcangle_other3.6925.7464359
X-RAY DIFFRACTIONr_scbond_it2.3694.1813253
X-RAY DIFFRACTIONr_scbond_other2.3694.1833254
X-RAY DIFFRACTIONr_scangle_it3.8126.0984808
X-RAY DIFFRACTIONr_scangle_other3.8126.14809
X-RAY DIFFRACTIONr_lrange_it6.47543.936709
X-RAY DIFFRACTIONr_lrange_other6.47543.9376709
X-RAY DIFFRACTIONr_ncsr_local_group_10.1010.056332
X-RAY DIFFRACTIONr_ncsr_local_group_20.090.056011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.4391900.4083263X-RAY DIFFRACTION99.9421
2.462-2.5290.3751730.3883216X-RAY DIFFRACTION99.8821
2.529-2.6030.4451360.383147X-RAY DIFFRACTION99.9696
2.603-2.6820.3191400.3253029X-RAY DIFFRACTION99.9369
2.682-2.770.3191190.3093007X-RAY DIFFRACTION100
2.77-2.8670.3091160.2792870X-RAY DIFFRACTION99.9665
2.867-2.9750.2811910.2492753X-RAY DIFFRACTION99.966
2.975-3.0960.2991530.2312591X-RAY DIFFRACTION99.9636
3.096-3.2330.2611080.2112569X-RAY DIFFRACTION100
3.233-3.390.2331400.2012457X-RAY DIFFRACTION100
3.39-3.5730.2361340.1962293X-RAY DIFFRACTION100
3.573-3.7880.223750.1762238X-RAY DIFFRACTION100
3.788-4.0480.2351510.1822019X-RAY DIFFRACTION100
4.048-4.370.2081030.1691936X-RAY DIFFRACTION99.951
4.37-4.7830.1861020.1441773X-RAY DIFFRACTION100
4.783-5.3420.227740.1421643X-RAY DIFFRACTION100
5.342-6.1570.221060.1761418X-RAY DIFFRACTION100
6.157-7.5120.216610.1781237X-RAY DIFFRACTION100
7.512-10.5050.166620.141952X-RAY DIFFRACTION100
10.505-49.9010.188340.231591X-RAY DIFFRACTION100
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)
13.11290.3410.65061.32370.0580.854-0.01580.12660.0254-0.06010.0068-0.03890.1669-0.03420.0090.07740.0080.02920.02510.01440.433326.3719-13.169749.2213
22.21691.47330.36573.37090.63430.9729-0.03940.00930.1021-0.0186-0.00210.02380.0930.12160.04150.0260.03360.00890.04680.03710.40612.3031-29.611956.867
33.5287-1.60442.63872.1693-1.27253.0190.1610.2898-0.1717-0.3780.00690.030.34160.0389-0.16790.22570.01030.01510.1003-0.03990.493428.6605-27.002138.2021
41.12190.410.55693.5772.14772.72680.046-0.1524-0.09540.048-0.0146-0.22890.14410.1118-0.03140.04060.0586-0.01330.13680.05920.557313.9815-37.593767.9019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLHHH1 - 217
2X-RAY DIFFRACTION2ALLIII1 - 216
3X-RAY DIFFRACTION3ALLLLL2 - 211
4X-RAY DIFFRACTION4ALLMMM2 - 210

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