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- PDB-3fcs: Structure of complete ectodomain of integrin aIIBb3 -

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Basic information

Entry
Database: PDB / ID: 3fcs
TitleStructure of complete ectodomain of integrin aIIBb3
Components
  • Integrin beta-3
  • Integrin, alpha 2b
KeywordsCell Adhesion/BLOOD CLOTTING / beta propeller / rossmann fold / egf domain / Cell adhesion / Disease mutation / Glycoprotein / Host-virus interaction / Integrin / Membrane / Phosphoprotein / Receptor / Transmembrane / Cell Adhesion-immune System COMPLEX / Cell Adhesion-BLOOD CLOTTING COMPLEX
Function / homology
Function and homology information


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 / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...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 / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / alphav-beta3 integrin-IGF-1-IGF1R complex / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / smooth muscle cell migration / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Signaling by RAF1 mutants
Similarity search - Function
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / 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 / Hormone receptor fold / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / 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 / Hormone receptor fold / 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 beta tail domain / : / 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 / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / 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) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Integrin beta-3 / Integrin alpha-IIb / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhu, J. / Luo, B.-H. / Xiao, T. / Zhang, C. / Nishida, N. / Springer, T.A.
CitationJournal: Mol.Cell / Year: 2008
Title: Structure of a complete integrin ectodomain in a physiologic resting state and activation and deactivation by applied forces.
Authors: Zhu, J. / Luo, B.H. / Xiao, T. / Zhang, C. / Nishida, N. / Springer, T.A.
History
DepositionNov 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin, alpha 2b
B: Integrin beta-3
C: Integrin, alpha 2b
D: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)368,90241
Polymers361,5554
Non-polymers7,34737
Water12,214678
1
A: Integrin, alpha 2b
B: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,68918
Polymers180,7782
Non-polymers3,91116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-13 kcal/mol
Surface area74630 Å2
MethodPISA
2
C: Integrin, alpha 2b
D: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,21423
Polymers180,7782
Non-polymers3,43621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-21 kcal/mol
Surface area68970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.300, 81.300, 654.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14A
24C
15B
25D
16B
26D
17B
27D
18B
28D
19B
29D
110B
210D
111B
211D
112A
212C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1112AA1 - 2211 - 221
2112CC1 - 2211 - 221
1212AA224 - 271224 - 271
2212CC224 - 271224 - 271
1312AA275 - 276275 - 276
2312CC275 - 276275 - 276
1412AA280 - 452280 - 452
2412CC280 - 452280 - 452
1122AA453 - 600453 - 600
2122CC453 - 600453 - 600
1132AA610 - 743610 - 743
2132CC610 - 743610 - 743
1144AA744 - 763744 - 763
2144CC744 - 763744 - 763
1244AA772 - 959772 - 959
2244CC772 - 959772 - 959
1154BB1 - 71 - 7
2154DD1 - 71 - 7
1256BB8 - 108 - 10
2256DD8 - 108 - 10
1354BB11 - 3211 - 32
2354DD11 - 3211 - 32
1454BB36 - 5736 - 57
2454DD36 - 5736 - 57
1554BB434 - 436434 - 436
2554DD434 - 436434 - 436
1164BB58 - 10858 - 108
2164DD58 - 10858 - 108
1264BB353 - 433353 - 433
2264DD353 - 433353 - 433
1174BB109 - 352109 - 352
2174DD109 - 352109 - 352
1184BB437 - 472437 - 472
2184DD437 - 472437 - 472
1194BB473 - 522473 - 522
2194DD473 - 522473 - 522
11104BB523 - 559523 - 559
21104DD523 - 559523 - 559
11114BB560 - 605560 - 605
21114DD560 - 605560 - 605
11125AA601 - 609601 - 609
21125CC601 - 609601 - 609

NCS ensembles :
ID
1
2
3
5
7
8
9
10
11
12
4
6
Detailshetero-dimer

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin, alpha 2b


Mass: 104460.719 Da / Num. of mol.: 2 / Fragment: UNP residues 32-989, Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B / Plasmid: pcDNA3.1, pEF1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): 3.2.8.1 / References: UniProt: Q17R67, UniProt: P08514*PLUS
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 76316.945 Da / Num. of mol.: 2 / Fragment: UNP residues 27-716, Extracellular domain / Mutation: P688C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

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Sugars , 5 types, 15 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.: 7
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-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/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
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: 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.: 5
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, 700 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 135066 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.55 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 12.17
Reflection shellResolution: 2.55→2.76 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.13 / Rsym value: 0.566 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.4.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Combination of PDB ENTRY 1JV2 and 1TXV

1jv2

1txv
PDB Unreleased entry


Resolution: 2.55→45.31 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 29.421 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26802 1785 1.3 %RANDOM
Rwork0.23285 ---
obs0.23332 133242 99.91 %-
all-135027 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error free: 0.297 Å / Luzzati sigma a free: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.55→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23654 0 462 678 24794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02224891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216841
X-RAY DIFFRACTIONr_angle_refined_deg0.7411.98533907
X-RAY DIFFRACTIONr_angle_other_deg0.6473.00740845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.26353122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.82624.5831104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.482153967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.95715151
X-RAY DIFFRACTIONr_chiral_restr0.0460.23794
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02127816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024792
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.88515479
X-RAY DIFFRACTIONr_mcbond_other0.15956292
X-RAY DIFFRACTIONr_mcangle_it1.5421024955
X-RAY DIFFRACTIONr_scbond_it0.77759412
X-RAY DIFFRACTIONr_scangle_it1.33108943
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2568TIGHT POSITIONAL0.050.25
1A3097MEDIUM POSITIONAL0.090.5
1A2568TIGHT THERMAL0.020.5
1A3097MEDIUM THERMAL0.022
2A871TIGHT POSITIONAL0.050.25
2A1026MEDIUM POSITIONAL0.10.5
2A871TIGHT THERMAL0.020.5
2A1026MEDIUM THERMAL0.012
3A774TIGHT POSITIONAL0.050.25
3A865MEDIUM POSITIONAL0.10.5
3A774TIGHT THERMAL0.010.5
3A865MEDIUM THERMAL0.012
4A2050MEDIUM POSITIONAL0.280.5
4A2050MEDIUM THERMAL0.092
5B663MEDIUM POSITIONAL0.20.5
5B41LOOSE POSITIONAL0.265
5B663MEDIUM THERMAL0.12
5B41LOOSE THERMAL0.0610
6B1719MEDIUM POSITIONAL0.170.5
6B1719MEDIUM THERMAL0.122
7B3174MEDIUM POSITIONAL0.170.5
7B3174MEDIUM THERMAL0.132
8B449MEDIUM POSITIONAL0.140.5
8B449MEDIUM THERMAL0.062
9B573MEDIUM POSITIONAL0.170.5
9B573MEDIUM THERMAL0.072
10B475MEDIUM POSITIONAL0.240.5
10B475MEDIUM THERMAL0.12
11B554MEDIUM POSITIONAL0.180.5
11B554MEDIUM THERMAL0.072
12A53MEDIUM POSITIONAL0.070.5
12A47LOOSE POSITIONAL0.115
12A53MEDIUM THERMAL0.082
12A47LOOSE THERMAL0.1310
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 127 -
Rwork0.411 8771 -
obs--100 %
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)
11.669-0.20910.35711.76580.43681.99830.02390.15890.0807-0.3133-0.1161-0.0579-0.0381-0.14430.0921-0.25360.0012-0.0395-0.0294-0.0057-0.0934-82.622-53.3398-79.4693
21.6977-0.07060.41831.5980.43652.0005-0.0925-0.14130.00290.01610.01480.0564-0.2180.0690.0776-0.1907-0.01610.044-0.3062-0.0659-0.23774.786334.0239.456
35.31481.49542.13812.31880.49585.44150.1148-0.3685-0.09660.06850.1690.2735-0.3069-0.1493-0.2838-0.0568-0.0079-0.0074-0.2487-0.2422-0.0129-47.4587-31.6025-42.6473
42.25491.8080.6765.42672.5665.47630.15260.00460.1531-0.37140.1093-0.0469-0.029-0.3162-0.2619-0.19040.0027-0.2075-0.1838-0.055-0.073-17.0567-1.0633-27.2439
52.640.65862.70433.23043.21517.8315-0.09590.0111-0.1684-0.590.12660.1128-0.6464-0.2333-0.0307-0.0614-0.0075-0.02550.0632-0.25090.0108-33.5079-40.0846-69.5152
63.41010.48643.15752.84492.80718.46510.0809-0.55020.12770.06140.035-0.1708-0.4495-0.648-0.11590.16610.0329-0.1624-0.18070.04380.0788-8.5684-15.1015-0.2543
71.5071-0.32890.16895.33033.8167.4174-0.132-0.26770.14660.15350.1325-0.2849-0.12660.0819-0.0005-0.1336-0.0842-0.1262-0.0461-0.1501-0.2978-43.4014-69.7992-114.9065
82.4053-1.23081.34040.7691-0.12642.99580.0772-1.519-0.60340.30890.3201-0.07780.029-0.7361-0.39740.73560.0093-0.30130.9487-0.02650.22521.0292-7.572944.5094
98.1591-1.55252.49363.3539-2.00833.87610.13680.02490.60870.209-0.1143-0.4263-0.64820.0285-0.02260.11380.0591-0.0546-0.1409-0.0051-0.1827-31.5571-73.4332-42.1754
104.1362-0.8401-0.68258.13293.19973.5169-0.21290.2341-0.144-0.43660.23540.67620.0488-0.7095-0.0225-0.09620.07160.00620.0323-0.1133-0.11524.7938-17.1445-27.7742
114.99491.57132.46412.44812.9644.76720.0126-0.205-0.60480.07430.00890.19760.76870.2044-0.02160.32660.1416-0.1422-0.55430.1004-0.0483-52.3761-87.7205-63.81
123.38791.52584.10946.24641.71356.31620.19030.1258-0.1564-0.17090.078-0.78490.33080.6615-0.2683-0.66040.18840.15730.3088-0.2235-0.036639.20563.7133-6.238
131.9253-0.7382-0.42312.14820.24850.73640.1690.4181-0.5928-0.0205-0.15490.35450.6881-0.2861-0.01410.3006-0.0992-0.1085-0.2293-0.18920.1094-80.6029-87.0349-83.1536
142.266-0.27050.02871.7838-0.63920.5997-0.11090.04690.14050.23870.1108-0.5378-0.31970.71320.0002-0.4633-0.0869-0.07710.2965-0.1614-0.020938.532231.829813.0841
152.6914-1.3749-3.06579.051-0.35583.9345-0.075-0.9920.40620.2852-0.09830.57560.1899-0.61630.1733-0.20240.128100.2486-0.1832-0.2543-39.2518-64.8909-28.2604
162.78551.0639-0.1642.61033.66569.36590.1380.55130.4349-1.143-0.27220.1319-0.7323-0.09130.13420.25350.0924-0.2294-0.12910.0398-0.191816.2263-9.3829-41.7377
179.18372.97811.60355.7373-0.48447.9206-0.2606-0.10070.30850.0753-0.1167-0.12950.14890.22690.3773-0.02820.195-0.0913-0.2974-0.23380.005-32.6151-51.2952-44.161
183.39561.0215-0.7028.9434-0.90116.4364-0.0497-0.0647-0.0109-0.0982-0.1751-0.04520.6239-0.0030.2248-0.24280.1658-0.2171-0.0823-0.07730.0812.6108-16.0107-25.8379
197.79674.21655.06777.18885.42069.35940.0016-0.13880.9855-0.3198-0.143-0.1647-0.3356-0.6620.14140.21480.0522-0.0408-0.48840.0023-0.0519-44.5219-61.884-63.7301
204.39934.3052.83535.60151.31586.1860.1729-0.2882-0.20510.01640.06571.0438-0.6047-0.1218-0.2386-0.27860.0926-0.05210.2574-0.05890.042213.1921-4.1175-6.2051
210.78730.0399-2.76943.42450.33679.8085-0.32190.3554-0.0970.185-0.10380.10550.347-0.12110.42570.03530.0667-0.06980.2095-0.1093-0.2329-45.0747-76.7271-89.5359
228.5751-0.9911.15392.0675-3.86347.27950.0954-0.04410.05330.7884-0.5623-0.64570.0451.0880.46690.5140-0.24230.1586-0.16470.009528.6652-4.534619.7967
230.22410.2408-0.71741.1316-0.2272.63450.4013-0.20370.90180.1321-0.4006-0.10231.1710.1712-0.00080.46780.03810.00820.4976-0.0190.6048-42.3353-95.3977-102.1487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 452
2X-RAY DIFFRACTION1A2004 - 2007
3X-RAY DIFFRACTION2C1 - 452
4X-RAY DIFFRACTION2C2004 - 2007
5X-RAY DIFFRACTION3A453 - 600
6X-RAY DIFFRACTION4C453 - 600
7X-RAY DIFFRACTION5A601 - 746
8X-RAY DIFFRACTION5A2008
9X-RAY DIFFRACTION6C601 - 746
10X-RAY DIFFRACTION6C2008
11X-RAY DIFFRACTION7A747 - 959
12X-RAY DIFFRACTION8C747 - 959
13X-RAY DIFFRACTION9B1 - 57
14X-RAY DIFFRACTION9B434 - 436
15X-RAY DIFFRACTION10D1 - 57
16X-RAY DIFFRACTION10D434 - 436
17X-RAY DIFFRACTION11B58 - 108
18X-RAY DIFFRACTION11B353 - 433
19X-RAY DIFFRACTION12D58 - 108
20X-RAY DIFFRACTION12D353 - 433
21X-RAY DIFFRACTION13B109 - 352
22X-RAY DIFFRACTION13B2001 - 2003
23X-RAY DIFFRACTION14D109 - 352
24X-RAY DIFFRACTION14D2001 - 2003
25X-RAY DIFFRACTION15B437 - 472
26X-RAY DIFFRACTION16D437 - 472
27X-RAY DIFFRACTION17B473 - 522
28X-RAY DIFFRACTION18D473 - 522
29X-RAY DIFFRACTION19B523 - 559
30X-RAY DIFFRACTION20D523 - 559
31X-RAY DIFFRACTION21B560 - 612
32X-RAY DIFFRACTION22D560 - 612
33X-RAY DIFFRACTION23B613 - 690

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