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- PDB-4mmz: Integrin AlphaVBeta3 ectodomain bound to an antagonistic tenth do... -

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Basic information

Entry
Database: PDB / ID: 4mmz
TitleIntegrin AlphaVBeta3 ectodomain bound to an antagonistic tenth domain of Fibronectin
Components
  • Fibronectin
  • Integrin alpha-V
  • Integrin beta-3
KeywordsCELL ADHESION / integrin / A domain / hybrid domain / PSI / EGF repeats / beta tail / calf / thigh / beta propeller / RGD motif / fibronectin / vitronectin
Function / homology
Function and homology information


integrin alphav-beta8 complex / negative regulation of monocyte activation / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / integrin alphav-beta1 complex ...integrin alphav-beta8 complex / negative regulation of monocyte activation / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / integrin alphav-beta1 complex / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / neural crest cell migration involved in autonomic nervous system development / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / peptidase activator activity / alphav-beta3 integrin-vitronectin complex / fibrinogen complex / regulation of extracellular matrix organization / Laminin interactions / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / peptide cross-linking / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / fibrinogen binding / entry into host cell by a symbiont-containing vacuole / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / integrin activation / negative regulation of lipid transport / ALK mutants bind TKIs / glycinergic synapse / angiogenesis involved in wound healing / regulation of phagocytosis / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-substrate junction assembly / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / positive regulation of vascular endothelial growth factor receptor signaling pathway / extracellular matrix binding / positive regulation of fibroblast migration / apolipoprotein A-I-mediated signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / regulation of bone resorption / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / smooth muscle cell migration / extracellular matrix structural constituent / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / MET activates PTK2 signaling / microvillus membrane / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / endodermal cell differentiation / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / negative regulation of macrophage derived foam cell differentiation / fibronectin binding / negative regulation of lipid storage / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans
Similarity search - Function
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / Hormone receptor fold / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 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 / von Willebrand factor, type A domain / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / 7 Propeller / Methylamine Dehydrogenase; Chain H / Kringle-like fold / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Fibronectin / Integrin beta-3 / Integrin alpha-V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
Authorsvan Agthoven, J. / Xiong, J. / Arnaout, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin.
Authors: Van Agthoven, J.F. / Xiong, J.P. / Alonso, J.L. / Rui, X. / Adair, B.D. / Goodman, S.L. / Arnaout, M.A.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 21, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / database_2 / diffrn / entity / entity_name_com / entity_src_gen / pdbx_audit_support / pdbx_branch_scheme / pdbx_contact_author / pdbx_database_status / pdbx_entity_branch_descriptor / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_entity_branch_descriptor.descriptor / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_all / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _reflns.number_all / _reflns.observed_criterion_sigma_I / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 3.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-V
B: Integrin beta-3
C: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,87928
Polymers193,1053
Non-polymers5,77325
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.792, 129.792, 307.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Integrin alpha-V / Vitronectin receptor / Vitronectin receptor subunit alpha


Mass: 106048.359 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 31-989)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P06756
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76523.125 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 27-718)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: P05106
#3: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 10533.767 Da / Num. of mol.: 1
Fragment: Fibronectin type-III domain 10 (UNP residues 1448-1540)
Mutation: GRGDSPAS to PRGDWNEG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pET / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02751

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Sugars , 4 types, 14 molecules

#4: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-beta-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
DManpa1-4DManpb1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{[(4+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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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

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Non-polymers , 4 types, 20 molecules

#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% PEG3350, 0.8 M sodium chloride, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 55243 / % possible obs: 99.9 % / Observed criterion σ(F): 5.4 / Redundancy: 6.1 % / Rsym value: 0.079 / Net I/σ(I): 24.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4873 / Rsym value: 0.739 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IJE

3ije


Resolution: 3.1→42.48 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 2706 4.9 %
Rwork0.2071 --
obs0.2093 55185 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13147 0 356 9 13512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.668
X-RAY DIFFRACTIONf_dihedral_angle_d13.6825141
X-RAY DIFFRACTIONf_chiral_restr0.0462123
X-RAY DIFFRACTIONf_plane_restr0.0042422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.160.34541140.29862760X-RAY DIFFRACTION100
3.16-3.220.32271750.27852689X-RAY DIFFRACTION100
3.22-3.280.3071290.2722693X-RAY DIFFRACTION100
3.29-3.360.32571510.2692745X-RAY DIFFRACTION100
3.36-3.430.33091330.28372738X-RAY DIFFRACTION100
3.43-3.520.29031490.26462752X-RAY DIFFRACTION100
3.52-3.620.30931430.24212700X-RAY DIFFRACTION100
3.62-3.720.29921270.22712752X-RAY DIFFRACTION100
3.72-3.840.30471200.2232744X-RAY DIFFRACTION100
3.84-3.980.24761500.22632732X-RAY DIFFRACTION100
3.98-4.140.25151330.21012764X-RAY DIFFRACTION100
4.14-4.330.22561400.19342783X-RAY DIFFRACTION100
4.33-4.550.22281400.17312722X-RAY DIFFRACTION100
4.55-4.840.19681550.16222779X-RAY DIFFRACTION100
4.84-5.210.23971640.16772758X-RAY DIFFRACTION100
5.21-5.730.21521570.1942752X-RAY DIFFRACTION100
5.74-6.560.27461470.21282824X-RAY DIFFRACTION100
6.56-8.260.24341560.21732840X-RAY DIFFRACTION100
8.26-42.480.25391230.18612952X-RAY DIFFRACTION98
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)
14.23391.32390.63083.2334-0.21731.8544-0.20450.11620.2833-0.02280.13880.1858-0.22250.00490.03740.8984-0.2263-0.05590.37260.03310.66965.936154.965723.0098
25.68970.83112.34-0.29110.0870.8836-0.29890.87550.3678-0.35920.16880.2641-0.12880.11810.08651.1022-0.3599-0.28720.93220.14851.2186-30.029447.6894-1.033
33.2348-0.66564.79341.1064-1.78038.8396-0.49290.27760.1814-0.16270.13690.1562-0.16260.24030.15970.8581-0.0077-0.07030.62050.00090.8727-46.297640.223632.1502
45.7846-3.48393.26377.0871-2.67954.8604-0.1504-0.44570.15170.69620.188-0.2891-0.17730.05360.01290.86740.19660.05890.4698-0.05560.7851-26.542438.116572.6983
52.76741.35410.37692.70270.14761.00070.12950.0504-0.68220.37730.0062-0.34840.2053-0.041-0.10651.102-0.1230.01620.42890.02810.8806-2.2416.40928.8353
62.72542.47694.01783.01624.76077.9089-0.7610.90930.5705-0.7760.29870.7128-0.55760.81010.5391.3809-0.1646-0.11951.09420.07591.3709-37.558323.003417.3131
72.53252.0156-0.57661.92431.00275.27790.0590.3620.60650.01750.2986-0.2213-0.2463-0.013-0.42471.14760.3327-0.07070.66080.04491.5557-10.262314.064666.7825
85.8707-2.63723.41634.77681.95465.37940.65533.47440.22714.21951.40880.79941.21794.0634-2.07642.3362-0.5702-0.15992.0989-0.64592.497525.952550.26456.8839
98.42742.1278-0.40447.529-5.93364.8684-0.7078-1.4579-2.77476.8843-1.2093-3.8727-1.2223-0.2461.44252.2868-0.3337-0.67452.46851.15452.388134.974637.016567.1224
107.6988-4.17276.43472.7261-4.92689.6371-1.2872-0.40170.05173.0592-1.1078-1.2296-1.48910.11531.7722.3323-0.082-0.65371.04370.28731.295126.426241.421361.3403
118.7757-0.50122.22864.89811.23795.6107-0.3885-1.1664-0.46571.6774-0.8085-1.4892-0.57311.36680.6451.6483-0.3771-0.60341.05780.49291.250428.915837.025452.6508
126.9892-3.998-0.71769.91453.0096.3336-0.13320.25470.54781.49480.3352-1.19130.32030.2187-0.10561.7023-0.3366-0.3680.94330.22811.393332.745433.935753.1832
138.9558-2.1159-4.18051.05711.00872.159-1.0425-1.7138-0.73352.41311.50530.20920.79950.1422-0.62592.29060.1357-0.80031.26860.51121.911638.69830.356761.7817
145.22095.7647-2.20688.08760.35045.431-0.054-0.6328-1.01651.8058-1.6724-1.2016-0.43660.57851.25721.9173-0.6501-0.85051.270.23521.611532.763639.978353.3183
157.8244-3.12685.54181.1916-2.17784.7760.4716-0.62840.98461.523-0.7618-2.1072-2.17120.85481.14091.7334-0.3603-0.58460.97550.10461.359328.622343.496350.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 342 )
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 598 )
3X-RAY DIFFRACTION3chain 'A' and (resid 599 through 764 )
4X-RAY DIFFRACTION4chain 'A' and (resid 765 through 954 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 445 )
6X-RAY DIFFRACTION6chain 'B' and (resid 446 through 606 )
7X-RAY DIFFRACTION7chain 'B' and (resid 607 through 690 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1417 through 1421 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1422 through 1431 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1432 through 1443 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1444 through 1453 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1454 through 1470 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1471 through 1482 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1483 through 1491 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1492 through 1507 )

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