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- PDB-6d4m: Crystal Structure of a Fc Fragment of Rhesus macaque (Macaca mula... -

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Basic information

Entry
Database: PDB / ID: 6d4m
TitleCrystal Structure of a Fc Fragment of Rhesus macaque (Macaca mulatta) IgG3
ComponentsFc fragment of IgG3
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG3 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsGohain, N. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
CitationJournal: Mabs / Year: 2019
Title: From Rhesus macaque to human: structural evolutionary pathways for immunoglobulin G subclasses.
Authors: Tolbert, W.D. / Subedi, G.P. / Gohain, N. / Lewis, G.K. / Patel, K.R. / Barb, A.W. / Pazgier, M.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fc fragment of IgG3
B: Fc fragment of IgG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1314
Polymers50,2052
Non-polymers2,9272
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint49 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.866, 65.866, 89.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Fc fragment of IgG3


Mass: 25102.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9746 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9746 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 5321 / % possible obs: 94.9 % / Redundancy: 2.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.172 / Net I/σ(I): 7.4
Reflection shellResolution: 3.45→3.5 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.3 / Rpim(I) all: 0.57 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AVE

3ave


Resolution: 3.47→35.114 Å / Cross valid method: FREE R-VALUE / σ(F): 3.2 / Phase error: 34.4
RfactorNum. reflection% reflection
Rfree0.2703 293 5.65 %
Rwork0.2491 --
obs0.2526 5308 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.47→35.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 198 0 3518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063632
X-RAY DIFFRACTIONf_angle_d1.0314989
X-RAY DIFFRACTIONf_dihedral_angle_d8.792187
X-RAY DIFFRACTIONf_chiral_restr0.057596
X-RAY DIFFRACTIONf_plane_restr0.008615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4702-3.81590.28891580.27172526X-RAY DIFFRACTION91
3.8159-4.35990.3031440.28252372X-RAY DIFFRACTION86
4.3599-5.46270.24551580.24832530X-RAY DIFFRACTION91
5.4627-17.01210.25761240.2262500X-RAY DIFFRACTION90
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.0378-0.05470.06480.11230.11210.0416-0.12380.2625-0.06070.373-0.2075-0.13320.4017-0.38760.4124-0.0002-0.26630.99840.12160.6972.99654.22916.7535
20.1401-0.0820.11590.00520.0643-0.0903-0.00720.0652-0.2221-0.2491-0.21230.0767-0.20280.23570.52410.0130.1910.93620.0011.014427.491818.8515.3509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 237 through 444)
2X-RAY DIFFRACTION2(chain 'B' and resid 236 through 444)

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