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- PDB-1vsg: 2.9 ANGSTROMS RESOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A ... -

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Basic information

Entry
Database: PDB / ID: 1vsg
Title2.9 ANGSTROMS RESOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A VARIANT SURFACE GLYCOPROTEIN FROM TRYPANOSOMA BRUCEI
ComponentsVARIANT SURFACE GLYCOPROTEIN MITAT 1.2
KeywordsGLYCOPROTEIN
Function / homology
Function and homology information


symbiont-mediated evasion of host immune response / side of membrane / plasma membrane
Similarity search - Function
Variant Surface Glycoprotein, subunit A; domain 2 / Variant Surface Glycoprotein, subunit A, domain 2 / Variant Surface Glycoprotein; Chain A domain 1 / Variant Surface Glycoprotein, subunit A domain 1 / Variant surface glycoprotein C-terminal domain superfamily / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Variant surface glycoprotein MITAT 1.2
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsFreymann, D. / Down, J. / Wiley, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: 2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei.
Authors: Freymann, D. / Down, J. / Carrington, M. / Roditi, I. / Turner, M. / Wiley, D.
#1: Journal: Nature / Year: 1987
Title: Two Variant Surface Gylcoproteins of Trypanosoma Brucei of Different Sequence Classes Have Similar 6 Angstroms Resolution X-Ray Structures
Authors: Metcalf, P. / Blum, M. / Freymann, D. / Turner, M. / Wiley, D.C.
#2: Journal: Nature / Year: 1984
Title: 6 Angstroms-Resolution X-Ray Structure of a Variable Surface Glycoprotein from Trypanosoma Brucei
Authors: Freymann, D.M. / Metcalf, P. / Turner, M. / Wiley, D.C.
History
DepositionOct 22, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / 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_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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
A: VARIANT SURFACE GLYCOPROTEIN MITAT 1.2
B: VARIANT SURFACE GLYCOPROTEIN MITAT 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8624
Polymers77,6892
Non-polymers1,1732
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-10 kcal/mol
Surface area27470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.500, 97.500, 123.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES ASN 183 - ASP 184, THR 265 - ALA 266, LYS 285 -GLU 289, AND ASP 328 - ASN 329 IN BOTH THE A CHAIN AND B CHAIN ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.06906, 0.19176, 0.97901), (0.19176, -0.9605, 0.20167), (0.97901, 0.20166, 0.02956)
Vector: 8.14443, -5.40635, -6.68537)
DetailsTHE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein VARIANT SURFACE GLYCOPROTEIN MITAT 1.2


Mass: 38844.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMTris-HCl1drop
30.01 %(w/v)1dropNaN3
458 %sat1reservoir(NH4)2SO4
520 mMTris-HCl1reservoir
60.01 %1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 24767 / Num. measured all: 56659 / Rmerge(I) obs: 0.087

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.22 / Highest resolution: 2.9 Å
Details: RESIDUES ASN 183 - ASP 184, THR 265 - ALA 266, LYS 285 -GLU 289, AND ASP 328 - ASN 329 IN BOTH THE A CHAIN AND B CHAIN ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 78 18 5508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.9 Å / Rfactor obs: 0.22 / Lowest resolution: 7 Å / Num. reflection obs: 5510
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.8
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_deg1.4

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