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- PDB-2vdq: Integrin AlphaIIbBeta3 Headpiece Bound to a Chimeric Fibrinogen G... -

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Basic information

Entry
Database: PDB / ID: 2vdq
TitleIntegrin AlphaIIbBeta3 Headpiece Bound to a Chimeric Fibrinogen Gamma chain peptide, HHLGGAKQRGDV
Components
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • FIBRINOGEN, GAMMA POLYPEPTIDE
  • 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


platelet maturation / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane ...platelet maturation / 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 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / fibrinogen complex / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / Regulation of TLR by endogenous ligand / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / platelet alpha granule / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / cellular response to interleukin-6 / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / MyD88 deficiency (TLR2/4) / apolipoprotein A-I-mediated signaling pathway / positive regulation of heterotypic cell-cell adhesion / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / IRAK4 deficiency (TLR2/4) / smooth muscle cell migration / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / microvillus membrane / extracellular matrix structural constituent / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / positive regulation of peptide hormone secretion / TGF-beta receptor signaling activates SMADs / positive regulation of exocytosis / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / protein secretion / protein polymerization / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / cellular response to interleukin-1 / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / fibrinolysis / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / response to 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 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. ...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 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / 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) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 alpha, N-terminal / Integrin domain superfamily / 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 2. / EGF-like domain signature 1. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fibrinogen gamma chain / Integrin beta-3 / Integrin alpha-IIb / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.59 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
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 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 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 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
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: FIBRINOGEN, GAMMA POLYPEPTIDE
H: MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN
L: MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,63619
Polymers148,3785
Non-polymers3,25914
Water23,9961332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-74.3 kcal/mol
Surface area71880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)148.331, 148.331, 176.567
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 FIBRINOGEN, GAMMA POLYPEPTIDE


Mass: 1278.421 Da / Num. of mol.: 1 / Fragment: GAMMA CHAIN C-TERMINAL PEPTIDE, RESIDUES 426-437 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q53Y18, UniProt: P02679*PLUS

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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


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, 1341 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.: 1332 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN C, ALA 396 TO ARG
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. THERE IS A A408R MUTATION ACCORDING TO THE AUTHORS THE CORRECT CHAIN C SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 70906437 WHICH CORRESPONDS TO THE UNIPROT ENTRY Q53Y18

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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 SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07223
DetectorType: CUSTOM (SBC2 3K) / Detector: CCD / Date: Feb 28, 2005 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07223 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 416764 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.59→34.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.204 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3207 5.1 %RANDOM
Rwork0.141 ---
obs0.143 60283 92.2 %-
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: 41.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.59→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10339 0 205 1332 11876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211011
X-RAY DIFFRACTIONr_bond_other_d0.0010.027399
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.97915042
X-RAY DIFFRACTIONr_angle_other_deg0.7863.00417995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66651392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02424.25480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.618151734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861563
X-RAY DIFFRACTIONr_chiral_restr0.0630.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022182
X-RAY DIFFRACTIONr_nbd_refined0.1870.22167
X-RAY DIFFRACTIONr_nbd_other0.180.27952
X-RAY DIFFRACTIONr_nbtor_refined0.1740.25357
X-RAY DIFFRACTIONr_nbtor_other0.0810.25803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.21064
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.83157028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.921010991
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90254613
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.953104030
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: 2.59→2.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 172
Rwork0.256 3171
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)
15.1519-0.36781.17215.0488-0.3053.6863-0.03850.4202-0.4221-0.0407-0.3412-0.50860.47570.89680.3797-0.17870.11150.0870.05780.29060.0188129.99914.27471.979
22.40120.3354-0.80213.16823.73163.3830.1791-0.30310-0.0964-0.3707-0.1127-0.16890.04440.1915-0.19730.0036-0.0214-0.01440.1883-0.1091126.90929.63971.685
31.2436-0.596-0.48621.4073-0.72391.7709-0.0851-0.13450.0430.1812-0.1609-0.33360.00190.43270.246-0.137-0.0652-0.03530.01920.1571-0.0122121.11730.81464.907
42.40720.3592-1.64361.5037-0.29232.53310.00720.0379-0.1503-0.0011-0.20120.2352-0.00550.03280.194-0.112-0.0791-0.0354-0.03830.0961-0.0803107.29436.0863.013
51.05670.2732-0.62431.2248-0.67722.11110.01650.1411-0.09510.0331-0.1469-0.00120.209-0.11460.1304-0.0788-0.05710.0054-0.05830.066-0.0321105.77524.96164.189
61.8569-0.21020.18432.1080.45121.9814-0.11050.1435-0.3214-0.0541-0.13590.04940.4135-0.12820.24650.0473-0.11510.0776-0.18450.0796-0.0614102.43910.72873.697
72.1365-0.7694-1.79637.16956.61969.1865-0.2291-0.3808-0.36850.3813-0.58680.42930.7645-0.90960.81590.1279-0.14250.1305-0.13880.1937-0.0602104.1124.80586.109
83.0515-0.1103-0.14493.28380.39752.6375-0.0857-0.0342-0.3666-0.1005-0.1327-0.23890.59760.22940.21830.07450.01570.0675-0.2220.2146-0.0559113.6493.63379.629
92.33630.1782-0.6422.7976-0.13942.43-0.1123-0.2174-0.40540.2705-0.2252-0.42570.60460.61740.3375-0.00930.11910.0202-0.03880.2936-0.003124.5077.67780.126
106.235-2.31563.993714.3805-1.25215.1649-0.1259-0.197-0.03841.40730.3054-0.6692-0.27360.2443-0.17950.44860.0164-0.3453-0.4309-0.0931-0.2413113.817.036172.178
113.2746-0.81741.71912.0407-0.60762.2909-0.226-0.8079-0.00660.96780.5002-0.0709-1.2238-1.5571-0.27420.73020.2532-0.0327-0.0102-0.0552-0.3091102.3223.435167.49
128.2655-2.827616.70477.6482-10.217936.7959-1.0577-0.6040.5161.30680.4407-0.3001-3.304-1.36570.6170.52580.16620.041-0.0713-0.0023-0.3133102.30129.901148.397
131.1865-0.73320.79160.6094-1.37065.4983-0.1074-0.15720.05110.4877-0.08650.0445-0.42820.1160.1940.2543-0.20060.0686-0.07240.0119-0.10293.93537.055108.079
141.2960.0436-1.51970.9821-0.56244.69230.1561-0.15480.18290.4261-0.0306-0.0659-0.59960.2147-0.12550.1063-0.17740.0201-0.12250.013-0.1318101.2643.11594.876
151.5493-0.5912-0.8141.84640.18122.0068-0.0193-0.30550.06520.4279-0.0598-0.09810.02380.24930.07910.0491-0.1644-0.0101-0.0650.066-0.1562102.46231.5197.102
162.8048-1.63376.68712.5615-4.270719.70610.7710.5888-0.458-0.37560.0546-0.1431.5450.9774-0.82560.2288-0.03990.0243-0.1804-0.0084-0.2087101.52821.694133.012
173.3091-0.64515.07431.7811-0.994116.7006-0.23390.48190.12020.67570.3232-0.3835-1.72640.92-0.08930.4416-0.0648-0.0475-0.38110.0318-0.2293108.48828.482149.861
186.4814-8.72065.702312.9537-8.67835.8462-0.479-0.33720.73572.5891-0.9301-2.9384-0.45423.03961.40911.7696-0.3199-0.65141.0824-0.07870.6805119.69430.898184.514
196.2129-3.70543.26116.5952-3.77586.4030.11350.2041-0.4749-0.17970.00110.21370.659-0.1045-0.1146-0.1584-0.1632-0.0325-0.04270.0509-0.059489.70436.18437.977
202.5888-0.25640.89720.5146-0.73482.9964-0.0770.04240.0811-0.02440.00110.04080.1133-0.17120.0759-0.15-0.0551-0.0069-0.02010.0745-0.054993.59843.85741.065
215.6097-0.0641-1.3612.1076-0.189410.55640.22330.0699-0.2752-0.2555-0.0670.04160.7554-0.1287-0.1563-0.18530.0971-0.0786-0.12880.0153-0.183391.78146.95.742
226.3754-0.2426-3.2762.37291.48329.1575-0.00170.4591-0.8232-0.9248-0.21490.18391.39920.01360.21660.15590.1211-0.1144-0.0254-0.1121-0.191790.74342.461-2.847
232.89160.4356-0.66270.8321-0.29773.11320.04850.33960.0734-0.11430.0269-0.09320.194-0.0075-0.0753-0.15270.0129-0.0032-0.01980.103-0.0507112.9245.43335.316
244.8024-3.8363.51124.67-3.09594.5960.15520.14780.3314-0.1327-0.2888-0.21260.28170.41450.1335-0.23980.06320.02860.1780.031-0.2399.59557.8735.346
257.1771-4.02313.0624.3622-2.49834.8740.03870.0186-0.2004-0.11310.01120.13350.020.1143-0.0499-0.25530.0159-0.00460.07160.0069-0.212995.91757.1975.475
2613.4686-5.52797.42564.434-5.0839.12530.46081.3891-0.0285-0.4251-0.6294-0.4311-0.06131.01020.1686-0.17540.16580.05580.20330.1594-0.1359102.64462.617-1.392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 54
3X-RAY DIFFRACTION3A55 - 115
4X-RAY DIFFRACTION4A116 - 164
5X-RAY DIFFRACTION5A165 - 243
6X-RAY DIFFRACTION6A244 - 315
7X-RAY DIFFRACTION7A316 - 337
8X-RAY DIFFRACTION8A338 - 376
9X-RAY DIFFRACTION9A377 - 452
10X-RAY DIFFRACTION10B1 - 28
11X-RAY DIFFRACTION11B29 - 72
12X-RAY DIFFRACTION12B79 - 100
13X-RAY DIFFRACTION13B101 - 137
14X-RAY DIFFRACTION14B138 - 201
15X-RAY DIFFRACTION15B202 - 342
16X-RAY DIFFRACTION16B343 - 390
17X-RAY DIFFRACTION17B391 - 441
18X-RAY DIFFRACTION18B442 - 461
19X-RAY DIFFRACTION19H1 - 31
20X-RAY DIFFRACTION20H32 - 122
21X-RAY DIFFRACTION21H123 - 185
22X-RAY DIFFRACTION22H186 - 221
23X-RAY DIFFRACTION23L1 - 104
24X-RAY DIFFRACTION24L105 - 160
25X-RAY DIFFRACTION25L161 - 192
26X-RAY DIFFRACTION26L193 - 214

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