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- PDB-5es4: RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BE... -

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Basic information

Entry
Database: PDB / ID: 5es4
TitleRE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION
Components
  • Integrin alpha-X
  • Integrin beta-2
KeywordsCELL ADHESION / Complement Receptor-4 alphaXbeta2
Function / homology
Function and homology information


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / complement component C3b binding / neutrophil migration ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / phagocytosis, engulfment / leukocyte cell-cell adhesion / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / heat shock protein binding / receptor-mediated endocytosis / cell adhesion molecule binding / cell-matrix adhesion / neutrophil chemotaxis / secretory granule membrane / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / animal organ morphogenesis / receptor internalization / cell-cell adhesion / receptor tyrosine kinase binding / positive regulation of angiogenesis / extracellular vesicle / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell-cell signaling / signaling receptor activity / amyloid-beta binding / regulation of cell shape / defense response to virus / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-2 / Integrin alpha-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsSen, M. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI CA031798 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.
Authors: Sen, M. / Springer, T.A.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_audit_support / 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_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
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: Integrin alpha-X
B: Integrin beta-2
C: Integrin alpha-X
D: Integrin beta-2
E: Integrin alpha-X
F: Integrin beta-2
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)847,07169
Polymers824,9498
Non-polymers22,12261
Water1,20767
1
A: Integrin alpha-X
B: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,14118
Polymers206,2372
Non-polymers5,90416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-X
D: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,53016
Polymers206,2372
Non-polymers5,29314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Integrin alpha-X
F: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,42717
Polymers206,2372
Non-polymers5,19015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Integrin alpha-X
H: Integrin beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,97318
Polymers206,2372
Non-polymers5,73516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.030, 163.480, 536.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Integrin alpha-X / CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain ...CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95


Mass: 125606.438 Da / Num. of mol.: 4 / Fragment: UNP residues 20-1103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAX, CD11C / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P20702
#2: Protein
Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 80630.695 Da / Num. of mol.: 4 / Fragment: UNP residues 23-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05107

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Sugars , 13 types, 44 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e6-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 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)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1_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]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f6-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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 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)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#17: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 84 molecules

#15: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#16: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, TEMPERATURE 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 198644 / % possible obs: 98.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 9.46
Reflection shellHighest resolution: 3.15 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.3→49.51 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1819 1.04 %Random selection
Rwork0.257 ---
obs0.258 174325 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49499 0 1432 67 50998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752369
X-RAY DIFFRACTIONf_angle_d1.18371193
X-RAY DIFFRACTIONf_dihedral_angle_d10.66231783
X-RAY DIFFRACTIONf_chiral_restr0.0688134
X-RAY DIFFRACTIONf_plane_restr0.0069200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38920.43751370.449712994X-RAY DIFFRACTION98
3.3892-3.48890.43331390.403813054X-RAY DIFFRACTION99
3.4889-3.60150.43231440.374813110X-RAY DIFFRACTION100
3.6015-3.73020.39781290.341213152X-RAY DIFFRACTION100
3.7302-3.87950.3711330.315413187X-RAY DIFFRACTION99
3.8795-4.0560.3471350.292913120X-RAY DIFFRACTION99
4.056-4.26970.30891400.274413243X-RAY DIFFRACTION100
4.2697-4.5370.28521560.236613235X-RAY DIFFRACTION100
4.537-4.8870.27641480.215213264X-RAY DIFFRACTION100
4.887-5.37830.29831390.224213305X-RAY DIFFRACTION100
5.3783-6.15530.31221260.247413411X-RAY DIFFRACTION100
6.1553-7.75020.31191570.272113539X-RAY DIFFRACTION100
7.7502-49.51230.25481360.214413892X-RAY DIFFRACTION100
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)
10.535-0.02810.424-0.0194-0.01361.97360.0710.28770.15360.53120.082-0.11480.2526-0.2792-0.00071.09070.1686-0.18970.88940.05831.0174-23.847519.0553-13.0643
20.0742-0.29790.43790.6161-0.36621.38610.2080.1018-0.0881-0.567-0.3229-0.00150.69080.663201.1710.0772-0.05840.99720.0620.9151-21.838713.132233.4337
31.80.9671-1.45030.7717-0.85561.0714-0.24470.2449-0.0668-0.22380.1569-0.07960.1134-0.114500.8846-0.085-0.00630.61250.0210.9151-2.902424.348149.6324
41.20290.4320.09392.42270.3704-0.20990.50140.27-0.3386-1.2947-0.2348-0.3760.70220.7436-0.03343.06120.97270.32940.7163-0.21491.4059-10.1912-17.461219.782
50.87521.2471.03250.04730.22680.7341-0.3774-0.0308-0.1027-1.25140.37980.10591.4433-0.08080.05893.15640.51090.38061.02460.01110.932-13.7293-10.01449.5107
60.74940.36790.25020.38350.40060.18260.41710.1674-0.6883-0.18160.2605-0.26811.2230.1080.00013.09610.59340.32711.74950.01361.9777-4.1412-22.648133.4044
70.2008-0.0336-0.04960.04020.0939-0.0507-0.1815-0.9226-0.05231.2020.1714-0.62470.49450.2607-0.00672.40390.07710.07551.09230.25451.5191-14.3511-20.87375.9306
80.01680.3339-0.22930.37440.02671.04130.16180.0115-0.0533-0.1410.033-0.0297-0.0560.37440.00011.60110.12520.10331.36440.19481.23663.56258.569731.4036
90.27910.01770.1562-0.04430.33312.10450.1392-0.5806-0.05720.33250.0623-0.29930.4669-0.42540.00131.0714-0.2065-0.34271.69710.12771.030424.254352.2123103.5674
101.27281.2282-0.6991.1934-0.4859-0.76760.228-0.7463-0.23080.4537-0.4739-0.2659-0.14660.4522-0.00010.9046-0.14-0.06081.11360.15250.97017.662626.929784.6488
111.8622-0.2240.83190.80540.32440.23550.0515-0.4489-0.31190.87120.2873-1.92680.5190.20020.4022.2710.5055-0.73951.50640.10062.541353.016819.136384.0506
120.53750.44540.19020.54660.82630.88050.2875-0.5803-0.10370.90770.1172-0.60850.5389-0.0545-0.00012.6140.2874-0.7392.4190.29781.948548.355728.003113.6542
130.06510.34420.16430.37160.25560.0550.2933-1.0831-1.39640.6804-0.40220.3491-0.3445-0.26460.00011.3118-0.13580.04361.87250.30051.673138.146637.382165.584
140.9561-0.340.4030.14250.14460.62290.02360.7308-0.6598-0.09150.9432-0.02751.2925-1.89160.00022.4834-0.2761-0.32432.31110.39561.808120.789610.3725111.4364
151.63970.2250.95170.38881.16923.2576-0.0589-0.93370.02940.3804-0.01450.02390.4358-0.2393-0.00030.8609-0.0844-0.0871.46740.02560.8845-32.977833.6309114.0189
160.24920.2898-0.13910.21420.11060.33930.1475-0.2997-0.02020.2743-0.14530.0107-0.01420.084300.7691-0.1658-0.19930.9888-0.05650.9558-23.232357.037187.2665
171.3326-0.2167-0.24691.89150.87520.5562-0.0904-0.81060.04660.04970.03630.80370.1534-1.15580.02011.50410.65850.07961.8722-0.56741.6818-68.345760.3004109.968
180.11430.2355-0.2831.4565-0.5176-0.0402-0.1709-1.1006-0.09440.1576-0.0144-0.0098-0.0501-0.332101.43490.198-0.10883.1606-0.4681.1526-50.623647.4628142.2594
191.0604-1.4932-0.85121.48760.61180.4418-0.2156-0.22590.26360.06590.174-0.0708-1.3949-0.3270.02460.74180.0958-0.17811.6206-0.37311.104-68.254556.4141100.2052
201.66070.9404-0.28520.1483-0.3347-0.04550.2429-0.5480.3130.2832-0.27510.2845-0.1578-0.4788-01.1586-0.183-0.05561.436-0.35061.1849-35.650866.5325106.0644
211.67840.34570.41591.08070.92571.45910.09630.27380.0629-1.0693-0.19380.1216-0.6160.255-01.48470.1494-0.1690.7402-0.02291.0635-2.557571.484516.2816
221.97840.24741.58111.06321.03930.35390.0148-0.04850.14880.0034-0.1111-0.0742-0.0987-0.4240.00020.6675-0.0137-0.0620.5679-0.01570.89164.087474.965366.7027
230.97060.59570.51620.77271.47442.3246-0.10920.4143-0.0448-0.25860.1849-0.1019-0.2487-0.0071-00.7835-0.0169-0.11880.94420.00421.0062-34.07353.807144.2472
240.17020.03330.16810.3981-0.2580.19830.2828-0.46660.3192-0.4477-0.04980.24220.1035-0.2548-02.27340.2301-0.30361.3884-0.25111.8285-16.576108.422664.322
251.2741-0.0348-1.16570.8021-0.93430.50410.2330.74840.29-0.87640.29010.32290.18910.03760.00013.09050.5616-0.53421.42280.16431.887-16.9773104.00764.3038
260.15340.4307-0.41710.03450.250.3869-0.3587-0.2886-0.2148-2.5386-0.01110.0209-1.4447-0.10860.00583.21110.5228-1.04671.3136-0.00261.3701-15.773998.14859.1884
270.44940.1389-0.15090.1504-0.38850.477-0.1498-1.256-0.09221.11450.04111.284-2.2460.4997-0.02052.61340.8671-0.35761.7754-0.44842.5923-23.373107.87729.2268
280.09490.2947-0.01510.2749-0.16710.0503-0.15030.06080.5736-0.163-0.2782-0.5553-1.0971-0.51520.00023.113-0.3613-0.43361.4163-0.02092.3566-4.8792116.58959.0051
290.7893-0.42640.1760.313-0.28250.1212-0.0216-0.4311-0.76570.26480.5813-0.2499-1.38440.27470.0391.9555-0.3163-0.07171.0582-0.24191.0899-3.665499.428477.1453
300.6602-0.1488-0.46820.12-0.12560.6020.39690.3452-0.00670.4741-0.0094-0.05420.4028-0.323301.4919-0.0186-0.2150.98550.03771.3437-29.302979.238137.6724
31-0.0784-0.0442-0.03730.0976-0.14130.16370.30580.943-0.21640.33790.6075-0.2494-0.07030.6374-0.00021.56220.0051-0.18391.0187-0.05721.3418-46.768863.546415.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 356 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 357 THROUGH 639 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 640 THROUGH 1080 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 213 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 214 THROUGH 360 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 361 THROUGH 431 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 432 THROUGH 482 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 483 THROUGH 674 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 1 THROUGH 691 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 692 THROUGH 1080 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 1 THROUGH 114 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 115 THROUGH 464 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 465 THROUGH 552 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 553 THROUGH 674 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 1 THROUGH 662 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 663 THROUGH 1080 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 1 THROUGH 138 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 139 THROUGH 329 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 330 THROUGH 482 )
20X-RAY DIFFRACTION20CHAIN 'F' AND (RESID 483 THROUGH 674 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 1 THROUGH 595 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 596 THROUGH 805 )
23X-RAY DIFFRACTION23CHAIN 'G' AND (RESID 806 THROUGH 1080 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 1 THROUGH 55 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 56 THROUGH 213 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 214 THROUGH 363 )
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 364 THROUGH 413 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 414 THROUGH 452 )
29X-RAY DIFFRACTION29CHAIN 'H' AND (RESID 453 THROUGH 497 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 498 THROUGH 637 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 638 THROUGH 674 )

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