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- PDB-5vf2: scFv 2D10 re-refined as a complex with trehalose replacing the or... -

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Basic information

Entry
Database: PDB / ID: 5vf2
TitlescFv 2D10 re-refined as a complex with trehalose replacing the original alpha-1,6-mannobiose
ComponentsscFv 2D10
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM RE-REFINEMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / trehalose
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsPorebski, P.J. / Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B.
Funding support United States, Austria, Poland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01HG008424, R01GM117080, R01GM117325 United States
Austrian Science FundP28395-B26 Austria
Polish National Science Centre2013/10/M/NZ1/00251 Poland
CitationJournal: Chemistryselect / Year: 2016
Title: Antibodies Can Exploit Molecular Crowding to Bind New Antigens at Noncanonical Paratope Positions
Authors: Vashisht, S. / Kumar, A. / Kaur, K.J. / Salunke, D.M.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Mar 21, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_comp_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 0THIS ENTRY 5VF2 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5I4F, DETERMINED BY S. ...THIS ENTRY 5VF2 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5I4F, DETERMINED BY S.VASHISHT,A.KUMAR,K.J.KAUR,D.M.SALUNKE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv 2D10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,79946
Polymers26,8951
Non-polymers90445
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.093, 81.093, 74.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2-

GLC

21A-569-

HOH

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Components

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Antibody / Sugars , 2 types, 3 molecules A

#1: Antibody scFv 2D10


Mass: 26894.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 323 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 41 / Source method: obtained synthetically
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.72 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5I4F
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES 6.5, Magnesium sulphate (1.5 M), potassium sodium tartrate tetrahydrate (0.1M).

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Data collection

DiffractionMean temperature: 173.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.549→50 Å / Num. obs: 41534 / % possible obs: 99.4 % / Redundancy: 5.5 % / Net I/σ(I): 39.67

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5I4F

5i4f


Resolution: 1.55→35.11 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.486 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18039 4100 10 %RANDOM
Rwork0.15284 ---
obs0.15561 37096 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 100 280 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022029
X-RAY DIFFRACTIONr_bond_other_d0.0020.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9822775
X-RAY DIFFRACTIONr_angle_other_deg0.9543.0014219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.225.038265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5324.4379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.792156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.54991
X-RAY DIFFRACTIONr_mcbond_other1.0471.541990
X-RAY DIFFRACTIONr_mcangle_it1.7662.3031246
X-RAY DIFFRACTIONr_mcangle_other1.7662.3031247
X-RAY DIFFRACTIONr_scbond_it1.4491.7441038
X-RAY DIFFRACTIONr_scbond_other1.4491.7441038
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2632.5571519
X-RAY DIFFRACTIONr_long_range_B_refined6.52720.7912288
X-RAY DIFFRACTIONr_long_range_B_other6.24519.7182237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 291 -
Rwork0.23 2722 -
obs--99.11 %
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)
10.8018-0.32180.79590.8388-0.13774.59130.0103-0.04210.06680.10730.01880.0606-0.4106-0.2053-0.02920.07510.01640.01730.04410.01790.067725.58713.6548.982
23.6579-0.59350.43452.6749-0.75943.22-0.0039-0.1935-0.22080.08640.09640.03770.0993-0.1857-0.09240.0608-0.01320.01390.03320.02120.049326.3184.2159.834
31.44670.2947-0.56090.9722-0.17415.02840.0652-0.2412-0.04040.17550.03950.0783-0.1771-0.0019-0.10460.04860.0083-0.00230.05050.01610.041230.4659.65713.508
41.62041.30920.91242.15291.2451.26260.03170.0305-0.05850.01650.005-0.0406-0.00260.0709-0.03670.0282-0.0068-0.00990.00990.00130.021247.9739.143.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 82
3X-RAY DIFFRACTION3A83 - 123
4X-RAY DIFFRACTION4A138 - 251

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