[English] 日本語
Yorodumi
- PDB-6srx: Structure of the arginase-2-inhibitory human antigen-binding frag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6srx
TitleStructure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021158
Components
  • Fab C0021158 heavy chain (IgG1)
  • Fab C0021158 light chain (IgG1)
KeywordsPROTEIN BINDING / arginase-2 inhibitor / IgG / antigen-binding fragment
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
HHH: Fab C0021158 heavy chain (IgG1)
LLL: Fab C0021158 light chain (IgG1)
III: Fab C0021158 heavy chain (IgG1)
MMM: Fab C0021158 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,87810
Polymers95,5714
Non-polymers3076
Water5,080282
1
HHH: Fab C0021158 heavy chain (IgG1)
LLL: Fab C0021158 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9395
Polymers47,7852
Non-polymers1543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-39 kcal/mol
Surface area20360 Å2
MethodPISA
2
III: Fab C0021158 heavy chain (IgG1)
MMM: Fab C0021158 light chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9395
Polymers47,7852
Non-polymers1543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-40 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.732, 122.670, 63.985
Angle α, β, γ (deg.)90.000, 114.891, 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

-
Components

#1: Antibody Fab C0021158 heavy chain (IgG1)


Mass: 24647.797 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 gen. sp. (Chinese hamster)
Strain (production host): ExpiCHO
#2: Antibody Fab C0021158 light chain (IgG1)


Mass: 23137.520 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 gen. sp. (Chinese hamster)
Strain (production host): ExpiCHO
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM NaAcO pH 5.0 20% PEG6000 200 mM LiCl

-
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: 1.9→48.96 Å / Num. obs: 67778 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4374 / CC1/2: 0.53 / % possible all: 98.5

-
Processing

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

6srv


Resolution: 1.9→48.955 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.373 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.193 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2609 3129 4.619 %
Rwork0.2337 --
all0.235 --
obs-67745 98.195 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.864 Å2
Baniso -1Baniso -2Baniso -3
1-1.237 Å20 Å21.324 Å2
2---0.705 Å20 Å2
3----1.231 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 18 282 6749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136685
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176028
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.6449133
X-RAY DIFFRACTIONr_angle_other_deg1.1761.56814077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93522.692260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5911526
X-RAY DIFFRACTIONr_chiral_restr0.0470.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021323
X-RAY DIFFRACTIONr_nbd_refined0.1760.2895
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.25401
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23141
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.23176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1790.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.212
X-RAY DIFFRACTIONr_nbd_other0.1510.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.260.210
X-RAY DIFFRACTIONr_mcbond_it1.1473.2013503
X-RAY DIFFRACTIONr_mcbond_other1.1433.1973498
X-RAY DIFFRACTIONr_mcangle_it2.0084.7874379
X-RAY DIFFRACTIONr_mcangle_other2.0094.7884380
X-RAY DIFFRACTIONr_scbond_it0.9433.2433182
X-RAY DIFFRACTIONr_scbond_other0.9433.2443183
X-RAY DIFFRACTIONr_scangle_it1.6294.8184754
X-RAY DIFFRACTIONr_scangle_other1.6294.8194755
X-RAY DIFFRACTIONr_lrange_it3.97436.5076817
X-RAY DIFFRACTIONr_lrange_other3.97336.5166818
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.056619
X-RAY DIFFRACTIONr_ncsr_local_group_20.0820.056177
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
1.9-1.9490.3542690.35147660.35251130.4860.48598.47450.359
1.949-2.0030.3422200.32846280.32949210.6640.68798.51660.333
2.003-2.0610.3851970.32145680.32448350.6950.73198.55220.324
2.061-2.1240.3141780.30743840.30746410.7580.77798.29780.307
2.124-2.1930.3551960.31542280.31745620.7540.78896.9750.312
2.193-2.270.3682150.31341150.31643890.7550.78798.65570.306
2.27-2.3560.3522010.31839420.3242090.7720.80198.43190.307
2.356-2.4520.3921890.29838330.30240820.7940.82798.53010.285
2.452-2.560.3081550.2936810.29139190.8350.86197.88210.274
2.56-2.6850.3171700.26834180.27137320.830.86996.14150.252
2.685-2.830.2881360.2433960.24235600.8920.90199.21350.227
2.83-3.0010.2741490.24132200.24233930.8910.90799.29270.233
3.001-3.2070.2791550.24629660.24831600.9050.90798.76580.239
3.207-3.4630.222980.23627590.23629580.9460.93596.58550.23
3.463-3.7910.2461390.21125470.21327170.9430.95198.8590.205
3.791-4.2360.1771070.16323410.16424760.9580.96798.86910.16
4.236-4.8850.1911100.13820370.14121830.9710.97798.35090.137
4.885-5.9680.1811110.16816730.16818310.9670.97397.43310.165
5.968-8.3780.2061150.18813240.1914520.9580.9699.10470.185
8.378-48.9550.246190.1917890.1938330.9410.95996.99880.194
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)
10.7171-0.9897-0.08551.84090.08840.26760.03380.0992-0.0204-0.0668-0.0389-0.06760.0430.02880.00510.0817-0.00270.06220.0482-0.03060.070520.9358-13.6668-9.7537
21.2629-1.80330.12862.5914-0.17650.230.13630.0906-0.2545-0.1869-0.1280.34550.1003-0.026-0.00830.1183-0.02610.06430.0799-0.04280.17918.6294-26.4079-13.3804
30.3796-0.61380.24222.1522-0.92080.61850.00710.07880.0451-0.0829-0.082-0.08430.00170.08190.07490.0805-0.02790.06030.03490.00160.0735-6.008837.745-22.8106
40.5431-0.76610.31961.7549-0.85640.4401-0.06180.00570.22660.271-0.1686-0.5225-0.16130.11670.23040.1671-0.053-0.00860.10610.00850.23845.083150.257-15.7058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLHHH1 - 214
2X-RAY DIFFRACTION2ALLLLL3 - 211
3X-RAY DIFFRACTION3ALLIII1 - 214
4X-RAY DIFFRACTION4ALLMMM1 - 210

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more