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- PDB-4mmx: Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibr... -

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Basic information

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


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / Extracellular matrix organization ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / peptidase activator activity / 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 / integrin alphaIIb-beta3 complex / fibrinogen complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / peptide cross-linking / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / integrin activation / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / ALK mutants bind TKIs / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of phagocytosis / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / proteoglycan binding / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / biological process involved in interaction with symbiont / extracellular matrix structural constituent / smooth muscle cell migration / Molecules associated with elastic fibres / MET activates PTK2 signaling / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / response to muscle activity / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / regulation of protein phosphorylation / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / basement membrane / negative regulation of lipid storage
Similarity search - Function
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Hormone receptor fold / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Hormone receptor fold / 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 / 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, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / 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 / Kringle-like fold / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / Fibronectin type 3 domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Few Secondary Structures / Irregular / Immunoglobulin-like fold / Immunoglobulins / 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: 3.32 Å
Authorsvan Agthoven, J. / Xiong, J. / Arnaout, M.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK088327 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK48549 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK096334 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK007540 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_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 / _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 2.1Nov 6, 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
Revision 3.0Mar 26, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn / entity_name_com / entity_src_gen / pdbx_audit_support / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
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_seq_id / _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] / _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_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_entity_branch_descriptor.descriptor / _pdbx_entry_details.has_ligand_of_interest / _pdbx_modification_feature.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _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_prop.value / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _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_low / _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 / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _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_sheet.id / _struct_sheet.number_strands
Description: Ligand geometry / Provider: author / Type: Coordinate replacement

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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)199,90825
Polymers192,9213
Non-polymers6,98722
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint56 kcal/mol
Surface area80080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.859, 129.859, 305.831
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: 10349.573 Da / Num. of mol.: 1
Fragment: Fibronectin type-III domain 10 (UNP residues 1448-1540)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P02751

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Sugars , 5 types, 14 molecules

#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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
#6: 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
#7: 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.: 2
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
#8: 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.: 5
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 , 2 types, 10 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
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: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2012
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.32→75.49 Å / Num. obs: 39593 / % possible obs: 88 % / Observed criterion σ(F): 5.3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.9
Reflection shellResolution: 3.32→3.41 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3003 / Rsym value: 0.676 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→42.51 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1942 4.91 %
Rwork0.2204 --
obs0.2227 39586 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13184 0 440 2 13626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313884
X-RAY DIFFRACTIONf_angle_d0.66118818
X-RAY DIFFRACTIONf_dihedral_angle_d14.1445221
X-RAY DIFFRACTIONf_chiral_restr0.0462172
X-RAY DIFFRACTIONf_plane_restr0.0052431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.40.33941470.29123003X-RAY DIFFRACTION100
3.4-3.490.3401850.30421356X-RAY DIFFRACTION46
3.5-3.60.34981660.28042984X-RAY DIFFRACTION100
3.6-3.710.3307470.26621222X-RAY DIFFRACTION40
3.71-3.850.28761270.25923018X-RAY DIFFRACTION100
3.85-40.3405820.24711431X-RAY DIFFRACTION47
4-4.180.25551520.23633046X-RAY DIFFRACTION100
4.18-4.40.22261380.20553033X-RAY DIFFRACTION100
4.4-4.680.22721730.17953029X-RAY DIFFRACTION100
4.68-5.040.23521750.18453027X-RAY DIFFRACTION100
5.04-5.540.2641840.20233037X-RAY DIFFRACTION100
5.55-6.340.27591590.23433077X-RAY DIFFRACTION100
6.35-7.980.29961680.23813125X-RAY DIFFRACTION100
7.99-42.510.25231390.19663256X-RAY DIFFRACTION99
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)
13.93531.08960.91333.124-0.41912.0635-0.36710.24140.246-0.21560.2242-0.0011-0.45120.13380.09810.6824-0.1872-0.0180.33780.00410.42747.670656.020522.336
24.54890.31071.8522-0.3864-0.06920.9806-0.12340.60090.193-0.2240.09190.2896-0.0275-0.01970.05390.9761-0.2907-0.21760.73140.12970.8911-27.351248.12751.3008
32.6108-0.38650.20532.5723-0.96914.531-0.1856-0.23390.0492-0.08840.15950.33810.20290.29360.04130.8022-0.0806-0.2010.64720.06730.7692-51.825242.506521.8485
44.7384-2.16742.99342.9277-2.69036.3691-0.0716-0.4505-0.10620.43350.08160.0008-0.00460.03380.06320.88370.24350.02660.4834-0.05280.6194-26.153336.538771.6902
58.2535-2.1775.73562.6451-2.29815.8901-0.09650.5244-0.9267-0.58140.39970.55390.0905-0.4742-0.73311.3352-0.3177-0.12240.7499-0.02591.2916-33.11742.377911.7887
62.36991.1957-0.05923.3805-0.83370.51950.1608-0.0393-1.13250.4558-0.1073-0.96550.21610.1661-0.01480.8483-0.0538-0.0490.41230.02930.81136.778215.519534.8642
70.76530.3219-0.36094.5054-1.33432.70170.08030.1331-0.8934-0.2080.2003-0.95180.28850.4473-0.21510.6773-0.0670.0050.4115-0.02791.079318.395427.14731.7515
83.59012.98920.35443.75490.7369-0.0741-0.0299-0.1628-0.37630.0335-0.1381-0.2870.2355-0.02470.15030.944-0.04880.01340.41130.07230.723-3.829818.647333.7537
95.8538-3.72053.69883.3047-3.28245.3050.6732.4297-0.17-1.7056-0.60390.23351.68710.27890.02621.8464-0.4379-0.17341.722-0.08540.939-30.55037.849-2.353
105.12410.04473.60871.96151.62214.7627-0.56380.57060.8659-0.7812-0.15250.96770.15540.170.8441.2245-0.2435-0.23480.90040.08391.3334-38.519424.392215.1967
115.534-6.56375.38877.559-6.1555.0272-0.1634-0.4913-0.0321-0.35920.2479-1.38480.1364-0.5099-0.11490.758-0.07390.09380.5601-0.04880.8977-18.562917.327658.9447
123.17992.2231.06181.76821.80046.0442-0.07940.2966-0.16880.10230.0651-0.4660.0820.6844-0.09961.23350.2758-0.08290.63830.08261.1463-7.555515.248968.4749
131.921-1.0069-1.35313.82573.62553.64450.7245-0.01210.34721.3589-0.2620.102-0.24130.6473-0.2692.41940.6952-0.91441.7061-0.47741.619627.267347.124461.9343
140.4740.35-0.21441.7762-2.5193.83870.1676-1.95431.4191.1427-1.55832.4025-1.62431.33870.91185.43161.3814-0.64733.7554-1.49642.481415.799546.26978.4372
155.2872-4.18426.54486.7594-6.40458.612-0.2782-1.31850.85781.7857-1.0161-0.83473.07030.54921.37262.0922-0.0127-0.05651.5862-0.06261.059918.506346.661260.1757
165.5659-1.42033.48112.86732.09045.7229-1.15471.75673.8551-1.3711-1.8971-0.3919-2.80920.43692.80862.61580.2557-0.38461.72110.29722.675716.124428.802468.508
176.644-5.4933-1.44895.19483.41037.80750.288-1.57-0.46192.4407-1.9082.67331.59182.01621.16041.7824-0.29860.45251.383-0.0381.010313.13848.271862.6543
188.20545.655-2.40614.0184-2.07052.12560.6342-0.61210.1349-1.1519-1.2851-1.5433.97022.76111.06452.07030.52460.42882.86481.01271.838714.430536.195376.3503
199.233-5.0404-7.40932.75094.04175.953-0.0594-3.44790.10832.82320.4587-0.93753.57160.2465-0.64732.9074-0.9684-0.12842.5225-0.47061.096319.500140.129461.7429
207.9706-4.9366-5.81824.76835.64756.6953-0.3368-1.4031.18961.31190.1868-2.8793.52591.04220.56421.4105-0.114-0.49420.83270.22771.096220.746941.653248.3364
210.61710.29960.00870.13980.0046-0.00171.9952-2.3012-0.32831.32460.42110.1357-5.48710.7547-2.02712.43690.15650.70323.36610.52051.539323.701238.732173.1529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 320 )
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 590 )
3X-RAY DIFFRACTION3chain 'A' and (resid 591 through 729 )
4X-RAY DIFFRACTION4chain 'A' and (resid 730 through 956 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 169 )
7X-RAY DIFFRACTION7chain 'B' and (resid 170 through 278 )
8X-RAY DIFFRACTION8chain 'B' and (resid 279 through 423 )
9X-RAY DIFFRACTION9chain 'B' and (resid 424 through 462 )
10X-RAY DIFFRACTION10chain 'B' and (resid 463 through 588 )
11X-RAY DIFFRACTION11chain 'B' and (resid 589 through 630 )
12X-RAY DIFFRACTION12chain 'B' and (resid 631 through 690 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1417 through 1425 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1426 through 1433 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1434 through 1452 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1453 through 1461 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1462 through 1473 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1474 through 1483 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1484 through 1490 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1491 through 1502 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1503 through 1509 )

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