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- PDB-4wk4: Metal Ion and Ligand Binding of Integrin -

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Basic information

Entry
Database: PDB / ID: 4wk4
TitleMetal Ion and Ligand Binding of Integrin
Components
  • ALA-CYS-ARG-GLY-ASP-GLY-TRP-CYS
  • Integrin alpha-5Integrin alpha 5
  • Integrin beta-1
KeywordsCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-FIBRONECTIN RECEPTOR / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / Formation of the ureteric bud / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / cardiac cell fate specification / C-X3-C chemokine binding / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / formation of radial glial scaffolds / Other semaphorin interactions / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / cell projection organization / myoblast fusion / vascular endothelial growth factor receptor 2 binding / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / platelet-derived growth factor receptor binding / axon extension / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / lamellipodium assembly / negative regulation of Rho protein signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / MET activates PTK2 signaling / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / epidermal growth factor receptor binding / sarcomere organization / positive regulation of wound healing / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / negative regulation of anoikis / RHOG GTPase cycle / intercalated disc / negative regulation of neuron differentiation / ECM proteoglycans / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / laminin binding / cellular defense response / coreceptor activity
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / 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 / : ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / 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) / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXia, W. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Metal ion and ligand binding of integrin alpha 5 beta 1.
Authors: Xia, W. / Springer, T.A.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 2.0Nov 22, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_conn / struct_keywords / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-5
B: Integrin beta-1
C: ALA-CYS-ARG-GLY-ASP-GLY-TRP-CYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,62120
Polymers98,2893
Non-polymers6,33117
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint3 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.520, 112.160, 169.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-5 / Integrin alpha 5 / CD49 antigen-like family member E / Fibronectin receptor subunit alpha / Integrin alpha-F / VLA-5


Mass: 47918.605 Da / Num. of mol.: 1 / Fragment: UNP residues 42-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA5, FNRA / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P08648
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 49502.852 Da / Num. of mol.: 1 / Fragment: UNP residues 21-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P05556

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ALA-CYS-ARG-GLY-ASP-GLY-TRP-CYS


Mass: 867.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Sugars , 6 types, 10 molecules

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


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
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
#11: 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.: 3 / Source method: obtained synthetically / 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, 195 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M HEPES 7.2, 16% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→47.6 Å / Num. obs: 38535 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 71.26 Å2 / Net I/σ(I): 7.17

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.597 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1996 5.18 %
Rwork0.1866 36535 -
obs0.1892 38531 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 387.85 Å2 / Biso mean: 104.0418 Å2 / Biso min: 35.27 Å2
Refinement stepCycle: final / Resolution: 2.5→47.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6829 0 779 188 7796
Biso mean--182.16 73.94 -
Num. residues----893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057468
X-RAY DIFFRACTIONf_angle_d0.98510115
X-RAY DIFFRACTIONf_chiral_restr0.0331183
X-RAY DIFFRACTIONf_plane_restr0.0031284
X-RAY DIFFRACTIONf_dihedral_angle_d12.0672764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56250.42011400.401525572697100
2.5625-2.63180.39471430.355826012744100
2.6318-2.70920.37061400.331325712711100
2.7092-2.79660.37351400.304425912731100
2.7966-2.89660.3151440.282426052749100
2.8966-3.01250.30361410.266425852726100
3.0125-3.14960.3031420.248626182760100
3.1496-3.31560.28241430.223425962739100
3.3156-3.52330.24631410.19826012742100
3.5233-3.79520.27481430.18362609275299
3.7952-4.1770.231430.15892629277299
4.177-4.78090.16161430.12682632277599
4.7809-6.02150.18781440.14662628277298
6.0215-47.60570.20921490.16462712286196
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)
14.695-1.16250.60716.95522.91046.874-0.21190.1287-0.9108-0.42380.19390.60340.897-1.3099-0.10840.4977-0.23060.0080.95450.02951.1471-7.2417-19.028-22.8646
24.18990.7752-0.45522.9267-0.21733.2357-0.0216-0.7439-0.33890.34250.04930.6762-0.2802-0.43960.01560.53630.11770.12740.83880.08170.69590.651-3.5789-8.8146
33.9650.09560.10462.91660.25372.4804-0.1457-0.0383-0.5508-0.25230.1570.11660.18560.0353-0.00430.4654-0.02770.05390.5068-0.02690.619415.3597-15.3899-23.6607
43.3302-1.084-0.24816.74040.06923.175-0.06860.4049-0.5772-0.37960.01341.12530.2065-0.6956-0.02280.6112-0.2141-0.11050.813-0.08920.9594-1.828-21.3527-30.7679
58.3474-2.67194.44388.4395-5.98915.1208-0.7516-0.3049-0.60991.360.24240.3962-0.514-0.17550.58331.7107-0.02980.09031.2103-0.22031.009816.92-32.8706-75.0477
67.22724.93710.37654.5975-2.12294.6307-0.01971.0783-1.1895-0.31790.7776-1.2091-0.22940.309-0.6781.80220.1180.33921.3608-0.22241.751520.7781-37.4844-83.1147
72.63681.5614-0.02126.70012.1720.9104-0.48580.57270.0813-1.7110.74880.44-0.62050.0073-0.23861.1736-0.1911-0.19690.990.06910.537721.94862.9629-72.0278
82.32020.4336-1.09843.04191.11266.6130.05210.13680.2604-0.6720.26010.1306-1.13320.4924-0.3590.5724-0.0275-0.07320.52380.07390.612323.46778.763-51.03
93.14971.3908-2.81261.732-2.30225.27050.5691-0.18710.94770.36390.07810.4023-1.14380.2695-0.61050.96590.04110.11880.53350.01050.811816.250319.9999-34.7216
106.93291.8301-3.46073.7484-2.20886.57510.01610.00770.31110.03660.16660.1778-0.1912-0.0788-0.09360.6128-0.0224-0.08280.4756-0.00030.510717.69947.4322-36.4283
113.59363.01672.82327.39587.02068.83790.47650.1568-0.04620.71180.1322-0.14580.78580.0884-0.69420.86470.0284-0.06130.7230.13430.634327.26931.3789-53.3398
127.85646.32013.1228.14593.79565.420.1675-0.1274-0.83070.2825-0.0082-0.99640.4451-0.0361-0.14530.92310.028-0.04220.8904-0.00060.700929.4226-4.8976-61.1763
139.50451.69892.04529.73727.09358.9067-0.36290.4581-0.283-0.0177-0.3481.4540.4-0.57560.64160.9256-0.1417-0.14940.90020.14530.589915.5829-6.1986-65.7158
149.104-4.93925.18645.2946-4.93454.6773-1.3369-0.9772.151.64370.3281-2.0364-2.18141.0921.07321.1475-0.2175-0.14340.8688-0.20.946223.151412.756-15.2935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 203 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 387 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 388 through 450 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 31 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 59 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 97 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 144 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 145 through 250 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 346 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 347 through 380 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 381 through 420 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 421 through 445 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 8 )C0

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