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

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Basic information

Entry
Database: PDB / ID: 6tul
TitleStructure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021177
Components(Fab C0021177 ...) x 2
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Function / homologyD-MALATE / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionJan 7, 2020Deposition 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: Fab C0021177 heavy chain (IgG1)
LLL: Fab C0021177 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9429
Polymers47,7022
Non-polymers1,2397
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-9 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.537, 69.244, 106.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HHHLLL

#1: Antibody Fab C0021177 heavy chain (IgG1)


Mass: 24605.717 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: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab C0021177 light chain (IgG1)


Mass: 23096.484 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)

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Non-polymers , 5 types, 52 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM MMT (D/L-malic acid, MES, tris) 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.25→47.83 Å / Num. obs: 19456 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 13.3 % / Rmerge(I) obs: 4.04 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1755 / CC1/2: 0.36 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SRV

6srv


Resolution: 2.25→47.505 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / SU B: 36.359 / SU ML: 0.395 / Cross valid method: FREE R-VALUE / ESU R: 0.459 / ESU R Free: 0.309
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3176 994 5.122 %
Rwork0.2482 --
all0.252 --
obs-19407 99.943 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.164 Å2
Baniso -1Baniso -2Baniso -3
1-4.928 Å20 Å20 Å2
2---3.131 Å20 Å2
3----1.796 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 83 45 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173059
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.6544555
X-RAY DIFFRACTIONr_angle_other_deg1.0391.587151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37322.8125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77115505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.271512
X-RAY DIFFRACTIONr_chiral_restr0.0310.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_nbd_refined0.1720.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1570.22847
X-RAY DIFFRACTIONr_nbtor_refined0.150.21542
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2120
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.228
X-RAY DIFFRACTIONr_nbd_other0.1860.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.212
X-RAY DIFFRACTIONr_mcbond_it0.6674.7221722
X-RAY DIFFRACTIONr_mcbond_other0.6674.7211721
X-RAY DIFFRACTIONr_mcangle_it1.2367.082149
X-RAY DIFFRACTIONr_mcangle_other1.2367.0812150
X-RAY DIFFRACTIONr_scbond_it0.3754.9031635
X-RAY DIFFRACTIONr_scbond_other0.3764.8931632
X-RAY DIFFRACTIONr_scangle_it0.7347.2452406
X-RAY DIFFRACTIONr_scangle_other0.7347.2412405
X-RAY DIFFRACTIONr_lrange_it3.15354.463354
X-RAY DIFFRACTIONr_lrange_other3.15354.4533354
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
2.25-2.3080.362530.38913510.38814040.4580.5271000.394
2.308-2.3720.324830.37612750.37313580.5130.5081000.377
2.372-2.440.352670.3612880.3613560.4910.52799.92630.363
2.44-2.5150.37790.34511990.34612780.5570.5971000.344
2.515-2.5970.348620.32112140.32212760.620.6951000.319
2.597-2.6880.413630.31211400.31812040.6930.76299.91690.302
2.688-2.7890.335660.29111150.29411810.830.8281000.274
2.789-2.9030.322440.28110920.28211360.7830.8321000.262
2.903-3.0310.452470.2810580.28611050.7180.8361000.252
3.031-3.1790.365550.2569930.26210480.8040.8611000.231
3.179-3.350.37660.2419330.2489990.790.8941000.223
3.35-3.5520.318450.2289070.2329520.8810.9081000.212
3.552-3.7950.301490.2248470.2298960.8820.9021000.212
3.795-4.0970.301400.248060.2438460.8690.8781000.228
4.097-4.4850.318420.27280.2077700.8820.9311000.2
4.485-5.0090.284410.26680.2047100.8950.93699.85920.205
5.009-5.7730.324270.2386060.2426340.8890.92899.84230.242
5.773-7.0450.273260.2385240.245500.9160.9211000.243
7.045-9.8550.24250.2044150.2064400.9530.9561000.215
9.855-47.5050.289140.252540.2522690.9060.94599.62830.271
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)
12.0846-0.2510.51840.8879-0.18623.94580.06410.1979-0.2073-0.1438-0.03650.29440.3146-0.1573-0.02760.0827-0.0305-0.040.13050.01810.1335-2.03953.28279.1324
21.21010.13491.46960.70920.04744.0676-0.15620.17610.12960.02980.013-0.0653-0.03350.30770.14320.0352-0.0104-0.02430.22930.00990.02373.171620.12828.1502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLHHH0 - 999
2X-RAY DIFFRACTION2ALLLLL0 - 999

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