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- PDB-2vdn: Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antago... -

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Basic information

Entry
Database: PDB / ID: 2vdn
TitleRe-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide
Components
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • EPTIFIBATIDE
  • INTEGRIN ALPHA-IIB
  • INTEGRIN BETA-3
KeywordsCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING / PLATELET INTEGRIN ALPHAIIBBETA3 / GLYCOPROTEIN / CELL ADHESION / MEMBRANE / INTEGRIN / RECEPTOR / ANTAGONIST / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION / DISEASE MUTATION / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / mesodermal cell differentiation / glycinergic synapse / extracellular matrix binding / filopodium membrane / regulation of release of sequestered calcium ion into cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell adhesion mediated by integrin / apolipoprotein A-I-mediated signaling pathway / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / positive regulation of leukocyte migration / wound healing, spreading of epidermal cells / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / cell adhesion mediated by integrin / smooth muscle cell migration / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / positive regulation of smooth muscle cell migration / negative chemotaxis / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / positive regulation of cell-matrix adhesion / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / protein disulfide isomerase activity / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / cellular response to platelet-derived growth factor stimulus / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell migration / cell adhesion molecule binding / positive regulation of smooth muscle cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell-cell adhesion / MAP2K and MAPK activation / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / ruffle membrane
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / 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 domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSpringer, T.A. / Zhu, J. / Xiao, T.
Citation
Journal: J.Cell Biol. / Year: 2008
Title: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.
Authors: Springer, T.A. / Zhu, J. / Xiao, T.
#1: Journal: Nature / Year: 2004
Title: Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics
Authors: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A.
History
DepositionOct 10, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionSep 2, 2008ID: 1TY6
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 28, 2016Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_chiral / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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 2.1Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRIN ALPHA-IIB
B: INTEGRIN BETA-3
C: EPTIFIBATIDE
H: MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN
L: MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,19119
Polymers147,9325
Non-polymers3,25914
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-75.7 kcal/mol
Surface area72070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)149.593, 149.593, 175.683
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 , 2 types, 2 molecules AB

#1: Protein INTEGRIN ALPHA-IIB / PLATELET MEMBRANE GLYCOPROTEIN IIB / GPALPHA IIB / GPIIB / INTEGRIN ALPHA-IIB HEAVY CHAIN


Mass: 49030.367 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 32-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08514
#2: Protein INTEGRIN BETA-3 / PLATELET MEMBRANE GLYCOPROTEIN IIIA / GPIIIA / CD61 ANTIGEN


Mass: 50969.664 Da / Num. of mol.: 1 / Fragment: HEADPIECE, RESIDUES 27-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P05106

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide EPTIFIBATIDE / MPT HRG GLY ASP TRP PRO CYS NH2


Mass: 832.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Antibody , 2 types, 2 molecules HL

#4: Antibody MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN


Mass: 23766.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C
#5: Antibody MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN


Mass: 23332.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: 10E5 HYBRIDOMA / Strain: BALB/C

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Sugars , 3 types, 5 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}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)]alpha-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]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/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
#10: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 373 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH ...ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH SHOULD BE USED IN PLACE OF P08514.

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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: 3.8 Å3/Da / Density % sol: 67.2 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 4, 2003 / Details: MIRROR
RadiationMonochromator: RH-COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 50647 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.9
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TXV

1txv
PDB Unreleased entry


Resolution: 2.9→47.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.178 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY6. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY6. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT BOUND LIGAND. THE MODEL IS REFINED TO LOWER RFREE. ONE SEQUENCE MISTAKE IN THE AIIB SUBUNIT IS CORRECTED. MORE OF BETA SUBUNIT DOMAIN I-EGF1 IS BUILT. MISTAKES IN CARBOHYDRATE ANOMERIC LINKAGES ARE ALSO CORRECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2421 5 %RANDOM
Rwork0.163 ---
obs0.166 46249 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10342 0 205 364 10911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210884
X-RAY DIFFRACTIONr_bond_other_d0.0010.027291
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.98314848
X-RAY DIFFRACTIONr_angle_other_deg0.7593.00517658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17451354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96824.356466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.724151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6321557
X-RAY DIFFRACTIONr_chiral_restr0.0570.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022142
X-RAY DIFFRACTIONr_nbd_refined0.1780.21959
X-RAY DIFFRACTIONr_nbd_other0.170.27414
X-RAY DIFFRACTIONr_nbtor_refined0.170.25286
X-RAY DIFFRACTIONr_nbtor_other0.0780.25662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.30256970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.141010835
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.21354568
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.062104006
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 140
Rwork0.283 3085
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)
14.9855-4.87240.76029.22180.4491.68370.04790.0961-0.5041.2353-0.4983-0.63480.51420.96560.45040.07410.12190.01550.29190.40470.129133.91412.70277.961
23.06751.18330.30713.8727-0.13141.95250.11680.0476-0.2906-0.1223-0.2987-0.41120.24660.26220.1819-0.14030.0750.04180.1670.2707-0.007129.94322.28168.597
31.3431-0.31390.10432.1599-1.31982.0259-0.0709-0.0302-0.03280.22-0.1243-0.50530.01330.49330.1951-0.1781-0.0454-0.0172-0.10110.1362-0.1279119.38134.01663.969
43.8617-0.5417-1.59732.34730.00842.63430.09810.1861-0.03150.0264-0.23480.04560.0357-0.02620.1368-0.1349-0.0952-0.0351-0.14230.0818-0.2223107.70136.48663.227
51.56320.169-0.79291.6179-1.10412.64450.0140.1007-0.24520.0345-0.1583-0.10050.2552-0.14940.1443-0.1385-0.06580.0007-0.17830.0524-0.1466106.80824.78263.451
61.8695-0.2032-0.12182.35610.36412.4832-0.04520.0949-0.4164-0.0916-0.0645-0.03660.2632-0.24580.10970.0765-0.13220.0536-0.15020.0406-0.0882100.53913.29571.796
73.1542-0.9411-0.55746.19621.86025.6722-0.1814-0.3245-0.55440.513-0.06570.03020.7186-0.00280.24710.0646-0.08230.0922-0.18050.20060.0388108.5837.42783.865
82.9228-0.7369-0.96433.78090.66764.279-0.1397-0.0458-0.4506-0.1773-0.2443-0.03880.7635-0.04760.3840.22220.02370.0872-0.14870.22920.0335111.4083.17378.204
93.27170.2069-0.73631.0976-0.20832.7013-0.1113-0.135-0.51320.1389-0.2413-0.56650.62390.60570.35260.18340.15440.03930.06080.31540.1523125.1887.87179.645
102.9026-1.33091.8522.8105-2.19866.8766-0.2105-0.6439-0.12351.12710.3333-0.0826-0.8495-0.7197-0.12281.08780.0182-0.15110.1867-0.06530.1719107.11521.142168.646
1111.9393-8.337521.854214.0434-20.686643.5833-0.5208-0.79230.14581.57930.77250.323-2.5266-1.7268-0.25170.85120.10420.02390.1488-0.0062-0.0191103.729.732149.283
120.2464-0.1432-0.10980.5425-1.26013.86540.0364-0.2941-0.06690.487-0.05830.0108-0.50660.09060.0220.2682-0.24190.0310.00840.0116-0.117497.93138.41103.816
131.3934-0.4453-1.34381.4175-0.04572.20150.0434-0.35480.06430.3429-0.1101-0.1166-0.15690.26420.06670.0561-0.1824-0.0178-0.04140.0664-0.1383103.53134.62995.625
143.1177-1.51737.97542.2141-4.31320.52820.64430.4708-0.3131-0.17450.0185-0.16771.63150.5024-0.66280.5076-0.07640.05180.20720.00180.1591100.63222.685130.342
154.213-0.69575.53771.2904-1.523616.2223-0.32610.49650.26560.84080.2831-0.538-1.68560.96870.0430.8908-0.1159-0.09650.05470.05070.2229109.82128.209148.575
163.1875-0.651-4.44731.8536-1.1788.7346-1.1091-1.96280.8840.88780.1138-1.225-1.38552.88960.99532.1005-0.33-0.52271.2511-0.0140.9544119.6531.262182.675
1710.7631-8.78276.003910.5748-6.15619.340.2710.7987-0.95-0.3808-0.02090.57360.59360.1377-0.2501-0.1012-0.224-0.0841-0.030.0452-0.052790.51537.1132.796
182.7059-0.35330.62781.3993-0.04562.50790.02350.0187-0.07860.06020.06090.22290.1624-0.2265-0.0844-0.2448-0.0519-0.0048-0.08670.0592-0.181794.65942.47440.807
193.298-0.35851.3481.0942-0.77732.9671-0.0631-0.03470.2173-0.014-0.0022-0.00360.1608-0.27040.0654-0.2045-0.07070.0298-0.07760.0591-0.174694.49443.31643.061
201.0449-1.1419-0.35562.05940.27894.64270.13630.4371-0.0933-0.1712-0.25460.0922-0.3474-0.37440.1183-0.2198-0.1-0.07920.12930.049-0.019786.84548.04812.584
218.82-0.7058-4.0960.88142.834311.31750.24470.4373-0.4141-0.2231-0.1889-0.08970.7652-0.0498-0.05580.06330.088-0.03030.03490.05220.064593.05945.2154.402
227.55281.6792-3.99151.9816-0.604715.90610.3456-0.53330.2213-0.4204-0.20840.06430.45490.378-0.1372-0.00070.0905-0.0442-0.02150.0315-0.115995.04247.9998.923
234.9617-1.31831.29383.42471.75521.77040.2750.3984-1.2056-0.3446-0.6613-0.01360.81450.57320.38630.81980.24770.00720.2833-0.02660.151894.4841.048-4.022
249.4756.2846-10.32156.4648-2.80923.1076-0.20180.5481-0.5947-1.07330.12170.67781.3684-1.0390.080.14010.0455-0.22510.3192-0.02270.144386.60344.203-2.243
250.91070.0216-2.10062.3351.83976.37480.08840.19630.1455-0.1132-0.0406-0.0389-0.13290.3619-0.0478-0.24330.03120.0206-0.06270.1525-0.0695114.88650.63334.842
263.49781.1665-0.91763.103-2.64622.43280.13510.3906-0.3091-0.1364-0.0271-0.09590.50940.0894-0.108-0.24510.0717-0.0167-0.10930.0182-0.1654114.22739.67535.812
274.1778-0.5453-2.03121.3949-0.4523.1205-0.01560.3796-0.0023-0.0853-0.04580.01950.3116-0.10020.0614-0.2454-0.005-0.0466-0.13430.0999-0.1267112.98146.21335.267
281.1735-1.44972.41742.4344-2.26565.78670.49440.335-0.3131-0.2805-0.22480.23810.64170.2813-0.2695-0.1510.02930.03140.20260.1054-0.0835100.94853.6847.874
296.806-5.36154.40048.4501-2.06853.3075-0.0895-0.34250.62470.0447-0.1484-0.55720.13630.28230.2379-0.2120.01090.02120.2860.1055-0.1393102.10460.2788.574
309.3678-4.64693.56734.9817-1.0833.6254-0.02390.3217-0.0162-0.321-0.1381-0.0136-0.05030.33520.1621-0.2016-0.0230.04970.17590.0363-0.195795.61860.6512.697
3111.7744-5.95831.40247.2184-4.61226.13780.47251.6877-0.3658-0.8299-0.6015-0.3561-0.11311.09880.129-0.06080.13980.13580.24650.1423-0.1685103.49463.085-2.293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 62
3X-RAY DIFFRACTION3A63 - 115
4X-RAY DIFFRACTION4A116 - 167
5X-RAY DIFFRACTION5A168 - 243
6X-RAY DIFFRACTION6A244 - 290
7X-RAY DIFFRACTION7A291 - 326
8X-RAY DIFFRACTION8A327 - 372
9X-RAY DIFFRACTION9A373 - 452
10X-RAY DIFFRACTION10B1 - 72
11X-RAY DIFFRACTION11B79 - 98
12X-RAY DIFFRACTION12B99 - 172
13X-RAY DIFFRACTION13B173 - 338
14X-RAY DIFFRACTION14B339 - 393
15X-RAY DIFFRACTION15B394 - 437
16X-RAY DIFFRACTION16B438 - 461
17X-RAY DIFFRACTION17H1 - 13
18X-RAY DIFFRACTION18H14 - 54
19X-RAY DIFFRACTION19H55 - 110
20X-RAY DIFFRACTION20H111 - 134
21X-RAY DIFFRACTION21H137 - 164
22X-RAY DIFFRACTION22H165 - 189
23X-RAY DIFFRACTION23H190 - 206
24X-RAY DIFFRACTION24H207 - 221
25X-RAY DIFFRACTION25L1 - 38
26X-RAY DIFFRACTION26L39 - 69
27X-RAY DIFFRACTION27L70 - 97
28X-RAY DIFFRACTION28L98 - 135
29X-RAY DIFFRACTION29L136 - 167
30X-RAY DIFFRACTION30L168 - 197
31X-RAY DIFFRACTION31L198 - 214

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