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- PDB-6mk0: Integrin AlphaVBeta3 ectodomain bound to antagonist TDI-4161 -

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Basic information

Entry
Database: PDB / ID: 6mk0
TitleIntegrin AlphaVBeta3 ectodomain bound to antagonist TDI-4161
Components
  • Integrin alpha-V
  • Integrin 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-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / tube development ...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 / opsonin binding / integrin alphav-beta1 complex / 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 / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / Laminin interactions / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / regulation of phagocytosis / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / transforming growth factor beta binding / platelet-derived growth factor receptor binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / negative regulation of low-density lipoprotein particle clearance / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / integrin complex / positive regulation of smooth muscle cell migration / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / cellular response to insulin-like growth factor stimulus / protein disulfide isomerase activity / regulation of postsynaptic neurotransmitter receptor internalization / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / endodermal cell differentiation / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / positive regulation of intracellular signal transduction / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / vasculogenesis / voltage-gated calcium channel activity / specific granule membrane / coreceptor activity / cell adhesion molecule binding / phagocytic vesicle / cellular response to platelet-derived growth factor stimulus / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / Integrin signaling / embryo implantation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration
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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain ...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 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / 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 / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / 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) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ribbon / Few Secondary Structures / Irregular / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-JUY / : / Integrin beta-3 / Integrin alpha-V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 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: Acs Pharmacol Transl Sci / Year: 2019
Title: Novel Pure alphaVbeta3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations
Authors: Li, J. / Fukase, Y. / Shang, Y. / Zou, W. / Munoz-Felix, J. / Buitrago, L. / van Agthoven, J. / Zhang, Y. / Hara, R. / Tanaka, Y. / Okamoto, R. / Yasui, T. / Nakahata, T. / Imaeda, T. / Aso, ...Authors: Li, J. / Fukase, Y. / Shang, Y. / Zou, W. / Munoz-Felix, J. / Buitrago, L. / van Agthoven, J. / Zhang, Y. / Hara, R. / Tanaka, Y. / Okamoto, R. / Yasui, T. / Nakahata, T. / Imaeda, T. / Aso, K. / Zhou, Y. / Locuson, C. / Nesic, D. / Duggan, M. / Takagi, J. / Vaughan, R.D. / Walz, T. / Hodivala-Dilke, K. / Teitelbaum, S.L. / Arnaout, M.A. / Filizola, M. / Foley, M.A. / Coller, B.S.
History
DepositionSep 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_refine_tls / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / 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.pdbx_formal_charge / _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] / _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 / _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_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _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 / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.pdbx_num_residues
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Feb 12, 2020Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _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.title / _citation.year
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_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 / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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.value / _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 / _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 3.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,64225
Polymers181,5842
Non-polymers6,05823
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint42 kcal/mol
Surface area73390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.406, 129.406, 305.535
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein 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 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76042.656 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

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Sugars , 4 types, 14 molecules

#3: 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-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
#4: 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-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]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c6-e1_e4-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)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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
#6: 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 , 3 types, 13 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-JUY / (2S)-2-[(1,3-benzothiazole-2-carbonyl)amino]-4-{[5-(1,8-naphthyridin-2-yl)pentanoyl]amino}butanoic acid


Mass: 491.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C25H25N5O4S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.06 Å3/Da / Density % sol: 69.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate pH 4.5, 800 mM Sodium Cholride, 12% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 59916 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.145 / Rsym value: 0.052 / Net I/σ(I): 23.2
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 5883 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IJE

3ije


Resolution: 3.005→49.094 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 2857 5.07 %
Rwork0.2215 53476 -
obs0.2231 56333 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.42 Å2 / Biso mean: 56.9907 Å2 / Biso min: 3.16 Å2
Refinement stepCycle: final / Resolution: 3.005→49.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12438 0 378 4 12820
Biso mean--67.51 37.72 -
Num. residues----1607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.005-3.05650.3539900.3112168260
3.0565-3.1120.33361170.2856202273
3.112-3.17190.31351170.2795224680
3.1719-3.23660.30671350.2789248387
3.2366-3.3070.33841310.2762254392
3.307-3.38390.29611460.2632264494
3.3839-3.46850.25941620.2664266996
3.4685-3.56230.32871320.2477276598
3.5623-3.6670.31061560.2338278799
3.667-3.78540.29931380.22762849100
3.7854-3.92060.24761340.22422851100
3.9206-4.07750.20951300.21152836100
4.0775-4.2630.20391860.19152778100
4.263-4.48760.19081720.18762855100
4.4876-4.76850.24481630.17332826100
4.7685-5.13640.20751540.17752845100
5.1364-5.65260.23591270.19842914100
5.6526-6.46890.2711600.22772892100
6.4689-8.14410.21661350.23272938100
8.1441-49.0940.23521720.213051100
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)
10.25750.2203-0.05750.536-0.07850.0936-0.07250.10690.0651-0.12720.09010.2295-0.0251-0.081-0.04210.3492-0.374-0.0760.0180.10410.14673.252853.682119.5111
21.3664-0.11050.48310.4640.0820.74-0.24540.24190.1688-0.11330.1471-0.0462-0.07610.17570.07250.6743-0.2117-0.38180.53060.17930.621-45.478746.4186-0.4572
31.4291-0.35972.19040.2047-0.70843.5562-0.28870.25180.2653-0.15390.04650.0749-0.05150.2510.1980.69760.0943-0.16650.49240.09590.4383-45.069640.956530.7352
41.1984-0.47310.11032.3251-0.46731.0264-0.1377-0.2495-0.08950.40280.1172-0.2268-0.05050.05330.03330.49180.2493-0.01480.2011-0.01340.2213-24.540937.245173.5242
51.75860.48482.16540.1870.56592.6846-0.10940.4797-0.2112-0.5112-0.02630.47120.1638-0.50520.12861.1193-0.01-0.19671.1559-0.01121.1124-41.55116.9777.3318
65.08430.38451.68251.63740.18982.19060.0740.325-0.4614-0.28440.041-0.01410.2757-0.1338-0.11180.6509-0.14530.03420.16420.04460.4201-16.73630.654123.1972
70.53370.6608-0.27451.733-0.140.68070.1427-0.2101-0.34960.2661-0.0552-0.44850.11680.12470.10770.4532-0.2033-0.12580.15730.14840.436613.871624.524334.473
82.3631-0.44260.51662.47060.68430.5347-0.07130.01380.0051-0.08650.01270.0931-0.1991-0.12430.05050.84740.00080.1150.22240.08830.4376-17.12411.011430.8911
91.1895-0.78750.27290.543-0.28081.3481-0.15110.59190.0698-0.4781-0.05180.4372-0.1742-0.46060.13881.0535-0.235-0.25820.71750.05850.892-38.632518.17944.1483
100.0926-0.11110.16620.5897-0.77121.0107-0.08430.1179-0.2001-0.06860.0189-0.00910.22180.0560.05030.67290.16540.00430.3273-0.06690.5301-19.937819.986846.9545
113.0595-0.0115-1.19733.6768-1.23253.85020.02940.06720.3035-0.1428-0.0847-0.4916-0.33630.26260.07170.67280.1622-0.01450.24570.08120.7851-7.184216.683470.8581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 444 )A1 - 444
2X-RAY DIFFRACTION2chain 'A' and (resid 445 through 647 )A445 - 647
3X-RAY DIFFRACTION3chain 'A' and (resid 648 through 755 )A648 - 755
4X-RAY DIFFRACTION4chain 'A' and (resid 756 through 954 )A756 - 954
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 43 )B4 - 43
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 111 )B44 - 111
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 365 )B112 - 365
8X-RAY DIFFRACTION8chain 'B' and (resid 366 through 412 )B366 - 412
9X-RAY DIFFRACTION9chain 'B' and (resid 413 through 538 )B413 - 538
10X-RAY DIFFRACTION10chain 'B' and (resid 539 through 642 )B539 - 642
11X-RAY DIFFRACTION11chain 'B' and (resid 643 through 690 )B643 - 690

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