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- PDB-6naj: Integrin AlphaVBeta3 ectodomain bound to Hr10 variant of the 10th... -

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Basic information

Entry
Database: PDB / ID: 6naj
TitleIntegrin AlphaVBeta3 ectodomain bound to Hr10 variant of the 10th domain of Fibronectin.
Components
  • Fibronectin, HR10 variant
  • Integrin alpha-VIntegrin alpha V
  • Integrin beta-3Integrin beta 3
KeywordsCELL ADHESION / HYBRID DOMAIN / PSI / EGF REPEATS / BETA TAIL / CALF / THIGH / BETA PROPELLER / RGD MOTIF / FIBRONECTIN / VITRONECTIN
Function / homology
Function and homology information


integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex ...integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / peptidase activator activity / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / regulation of extracellular matrix organization / platelet alpha granule membrane / fibrinogen complex / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / peptide cross-linking / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / integrin activation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / ALK mutants bind TKIs / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of phagocytosis / cell-substrate junction assembly / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / angiogenesis involved in wound healing / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell adhesion mediated by integrin / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / positive regulation of intracellular signal transduction / proteoglycan binding / positive regulation of cell-matrix adhesion / cell adhesion mediated by integrin / smooth muscle cell migration / microvillus membrane / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / endodermal cell differentiation / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / Non-integrin membrane-ECM interactions / fibronectin binding / Signaling by ALK fusions and activated point mutants / basement membrane / positive regulation of cell adhesion
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. / Fibronectin type-I domain profile. ...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 / 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) / 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 alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / 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 / 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 / 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. / Arnaout, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)K01DK101628-04 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure-guided design of pure orthosteric inhibitors of alpha IIb beta 3 that prevent thrombosis but preserve hemostasis.
Authors: Adair, B.D. / Alonso, J.L. / van Agthoven, J. / Hayes, V. / Ahn, H.S. / Yu, I.S. / Lin, S.W. / Xiong, J.P. / Poncz, M. / Arnaout, M.A.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / database_2 / entity / entity_src_gen / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_mon_prot_cis
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] / _audit_author.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_contact_author.id / _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_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _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.pdbx_method_to_determine_struct / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 3.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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, HR10 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,25025
Polymers191,4803
Non-polymers5,76922
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint47 kcal/mol
Surface area77900 Å2
Unit cell
Length a, b, c (Å)129.713, 129.713, 308.198
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 / Integrin alpha V / Vitronectin receptor / Vitronectin receptor subunit alpha


Mass: 105541.766 Da / Num. of mol.: 1
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) / References: UniProt: P06756
#2: Protein Integrin beta-3 / Integrin beta 3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76310.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P05106
#3: Protein Fibronectin, HR10 variant / / FN / Cold-insoluble globulin / CIG


Mass: 9627.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / 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.: 5
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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, 14 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.91 Å3/Da / Density % sol: 68.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 M Sodium Acetate, PEG4000, 800 mM Sodium Chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 55225 / % possible obs: 97 % / Redundancy: 8.2 % / Rmerge(I) obs: 9.7 / Net I/σ(I): 24.9
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 5959 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mmz

4mmz


Resolution: 3.1→49.62 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 2459 4.9 %
Rwork0.238 --
obs0.2394 50171 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13137 0 357 6 13500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.622
X-RAY DIFFRACTIONf_dihedral_angle_d13.8355137
X-RAY DIFFRACTIONf_chiral_restr0.0452126
X-RAY DIFFRACTIONf_plane_restr0.0042422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.160.3546620.31951597X-RAY DIFFRACTION54
3.16-3.230.3762930.30971698X-RAY DIFFRACTION60
3.23-3.30.31061170.29921964X-RAY DIFFRACTION69
3.3-3.380.3451360.28622146X-RAY DIFFRACTION76
3.38-3.460.3261060.28492402X-RAY DIFFRACTION83
3.46-3.550.31341360.27842690X-RAY DIFFRACTION93
3.55-3.660.28771500.28532843X-RAY DIFFRACTION99
3.66-3.780.29421590.25062883X-RAY DIFFRACTION100
3.78-3.910.27961360.24762919X-RAY DIFFRACTION100
3.91-4.070.28221320.22692910X-RAY DIFFRACTION100
4.07-4.250.27311690.21692868X-RAY DIFFRACTION100
4.25-4.480.22191670.2182920X-RAY DIFFRACTION100
4.48-4.760.22591640.19892888X-RAY DIFFRACTION100
4.76-5.120.21741600.19882911X-RAY DIFFRACTION100
5.12-5.640.22121360.22732965X-RAY DIFFRACTION100
5.64-6.450.27991480.24582947X-RAY DIFFRACTION100
6.45-8.120.24611490.25073010X-RAY DIFFRACTION100
8.12-49.620.27551390.21353151X-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)
10.7753-0.12510.14491.1874-0.19960.7001-0.16070.08180.0642-0.00770.2110.2109-0.2116-0.07430.12080.4259-0.61340.0587-0.38290.11020.07986.48355.3122.965
21.44410.07180.06650.09140.08920.0569-0.2350.64010.3671-0.5140.14790.2311-0.1873-0.08790.16860.789-0.4923-0.37480.47230.19570.6213-29.78948.25-0.68
3-0.0198-0.0060.0410.2071-0.18530.2381-0.3160.1933-0.1427-0.00370.1670.1157-0.08010.2811-0.01140.78320.147-0.20280.66140.01090.3854-45.80840.18532.546
40.88680.0784-0.53390.83830.29610.4772-0.0987-0.2355-0.16320.27620.0322-0.2509-0.0783-0.0379-0.00070.74440.3378-0.06990.24320.0230.3487-25.77337.73373.039
51.25710.0819-0.6141.9951-0.27250.91080.11110.0896-0.72830.07350.0639-0.27880.2331-0.10010.27530.7696-0.1482-0.0099-0.08520.15310.5932-1.46716.6928.468
60.2871-0.0176-0.00810.3430.18140.0907-0.25960.67820.2259-0.37820.070.73170.11570.0948-0.00351.2466-0.0747-0.24480.9533-0.091.2384-36.89223.25617.427
71.18040.26291.00990.88330.58991.02470.03350.33830.3996-0.38520.242-0.314-0.30170.26020.18190.86750.2745-0.01260.35640.13031.0475-9.42913.88666.853
80.0050.0023-0.00130.0038-00.00270.0158-0.01020.0036-0.02030.00490.0182-0.0007-0.0008-0.00011.1589-0.0852-0.11991.03270.03821.058127.88149.50555.941
90.00580.0023-0.00370.00530.00410.00880.033-0.0384-0.08290.03270.0108-0.0392-0.0266-0.025601.37440.18490.07621.1828-0.03311.38236.29135.31665.546
100.01890.01460.00010.01350.00560.0191-0.0865-0.0471-0.07760.03-0.1374-0.0795-0.0649-0.07590.00021.37580.1513-0.29881.12730.18991.365427.46240.87759.919
110.00350.0039-0.00260.0289-0.02010.0204-0.05970.0132-0.1143-0.01170.0097-0.34610.0150.10230.00010.9239-0.012-0.2160.72940.40531.019830.10636.71451.271
120.013-0.00160.01640.0337-0.00160.03170.09170.0664-0.0857-0.02690.1584-0.23840.03850.154-0.00021.2056-0.1921-0.01481.0470.12451.44133.62333.88351.74
130.0060.00160.00140.0136-0.00470.02080.0392-0.05530.01230.10720.0741-0.033-0.0364-0.0435-01.29820.14-0.15781.26720.16081.336640.11929.90858.916
140.00620.0063-0.00360.0091-0.00090.0097-0.0535-0.00740.01010.0273-0.01690.02820.03110.06770.00010.9674-0.0339-0.41140.77860.01261.04233.64639.65852.194
150.0074-0.00820.00130.0068-00.006-0.0438-0.1785-0.01110.0539-0.0307-0.14310.03150.263800.98370.0799-0.23590.73440.02620.673629.32442.64149.548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:342 )A1 - 342
2X-RAY DIFFRACTION2( CHAIN A AND RESID 343:598 )A343 - 598
3X-RAY DIFFRACTION3( CHAIN A AND RESID 599:764 )A599 - 764
4X-RAY DIFFRACTION4( CHAIN A AND RESID 765:954 )A765 - 954
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:445 )B1 - 445
6X-RAY DIFFRACTION6( CHAIN B AND RESID 446:606 )B446 - 606
7X-RAY DIFFRACTION7( CHAIN B AND RESID 607:690 )B607 - 690
8X-RAY DIFFRACTION8( CHAIN C AND RESID 1417:1421 )C1417 - 1421
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1422:1431 )C1422 - 1431
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1432:1443 )C1432 - 1443
11X-RAY DIFFRACTION11( CHAIN C AND RESID 1444:1453 )C1444 - 1453
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1454:1470 )C1454 - 1470
13X-RAY DIFFRACTION13( CHAIN C AND RESID 1471:1482 )C1471 - 1482
14X-RAY DIFFRACTION14( CHAIN C AND RESID 1483:1491 )C1483 - 1491
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1492:1506 )C1492 - 1506

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