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- PDB-3fcu: Structure of headpiece of integrin aIIBb3 in open conformation -

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Basic information

Entry
Database: PDB / ID: 3fcu
TitleStructure of headpiece of integrin aIIBb3 in open conformation
Components
  • Integrin beta-3
  • Integrin, alpha 2b
KeywordsCell Adhesion/BLOOD CLOTTING / CRYSTAL STRUCTURE / PLATELET INTEGRIN ALPHAIIBBETA3 / FIBRINOGEN BINDING / ALLOSTERY / THERAPEUTIC ANTAGONISM / Cell adhesion / Integrin / Membrane / Receptor / Transmembrane / Disease mutation / Glycoprotein / Host-virus interaction / Phosphoprotein / 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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / 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 / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / negative regulation of low-density lipoprotein particle clearance / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / regulation of bone resorption / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / integrin complex / positive regulation of smooth muscle cell migration / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / negative chemotaxis / positive regulation of cell-matrix adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / cell adhesion mediated by integrin / Syndecan interactions / positive regulation of osteoblast proliferation / p130Cas linkage to MAPK signaling for integrins / cellular response to insulin-like growth factor stimulus / regulation of postsynaptic neurotransmitter receptor internalization / 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 / ECM proteoglycans / Integrin cell surface interactions / 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 / Integrin signaling / embryo implantation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / 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 / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / cell-cell adhesion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to xenobiotic stimulus / integrin binding / positive regulation of fibroblast proliferation
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 beta tail domain / 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 / 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 beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin 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 / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Integrin beta-3 / Integrin alpha-IIb / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Version format compliance
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 / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 2.2Nov 27, 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
E: Integrin, alpha 2b
F: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,07544
Polymers301,4576
Non-polymers5,61838
Water5,368298
1
A: Integrin, alpha 2b
B: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,48615
Polymers100,4862
Non-polymers2,00113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-27 kcal/mol
Surface area39170 Å2
MethodPISA
2
C: Integrin, alpha 2b
D: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,32415
Polymers100,4862
Non-polymers1,83813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-44 kcal/mol
Surface area39010 Å2
MethodPISA
3
E: Integrin, alpha 2b
F: Integrin beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,26514
Polymers100,4862
Non-polymers1,77912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-43 kcal/mol
Surface area38830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)332.093, 332.093, 88.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12A
22C
32E
13A
23C
33E
14B
24D
34F
15B
25D
35F
16B
26D
36F
17B
27D
37F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYS5AA2 - 272 - 27
211ASNASNLYSLYS5CC2 - 272 - 27
311ASNASNLYSLYS5EE2 - 272 - 27
121VALVALLEULEU4AA33 - 4333 - 43
221VALVALLEULEU4CC33 - 4333 - 43
321VALVALLEULEU4EE33 - 4333 - 43
131GLNGLNTYRTYR4AA47 - 20747 - 207
231GLNGLNTYRTYR4CC47 - 20747 - 207
331GLNGLNTYRTYR4EE47 - 20747 - 207
141PROPROLEULEU4AA209 - 212209 - 212
241PROPROLEULEU4CC209 - 212209 - 212
341PROPROLEULEU4EE209 - 212209 - 212
151VALVALLEULEU4AA216 - 221216 - 221
251VALVALLEULEU4CC216 - 221216 - 221
351VALVALLEULEU4EE216 - 221216 - 221
112ASPASPASPASP5AA224 - 271224 - 271
212ASPASPASPASP5CC224 - 271224 - 271
312ASPASPASPASP5EE224 - 271224 - 271
113LEULEUGLNGLN5AA280 - 451280 - 451
213LEULEUGLNGLN5CC280 - 451280 - 451
313LEULEUGLNGLN5EE280 - 451280 - 451
114GLYGLYTHRTHR5BB1 - 71 - 7
214GLYGLYTHRTHR5DD1 - 71 - 7
314GLYGLYTHRTHR5FF1 - 71 - 7
124SERSERPROPRO5BB11 - 3211 - 32
224SERSERPROPRO5DD11 - 3211 - 32
324SERSERPROPRO5FF11 - 3211 - 32
134PROPROPROPRO5BB36 - 5736 - 57
234PROPROPROPRO5DD36 - 5736 - 57
334PROPROPROPRO5FF36 - 5736 - 57
144ASPASPALAALA5BB434 - 436434 - 436
244ASPASPALAALA5DD434 - 436434 - 436
344ASPASPALAALA5FF434 - 436434 - 436
115VALVALGLUGLU5BB58 - 10858 - 108
215VALVALGLUGLU5DD58 - 10858 - 108
315VALVALGLUGLU5FF58 - 10858 - 108
125SERSERCYSCYS5BB353 - 433353 - 433
225SERSERCYSCYS5DD353 - 433353 - 433
325SERSERCYSCYS5FF353 - 433353 - 433
116ASPASPARGARG5BB109 - 352109 - 352
216ASPASPARGARG5DD109 - 352109 - 352
316ASPASPARGARG5FF109 - 352109 - 352
117CYSCYSARGARG5BB437 - 461437 - 461
217CYSCYSARGARG5DD437 - 461437 - 461
317CYSCYSARGARG5FF437 - 461437 - 461

NCS ensembles :
ID
1
2
3
4
5
6
7
Detailsheter-dimer

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Integrin, alpha 2b


Mass: 49515.965 Da / Num. of mol.: 3 / Fragment: UNP residues 32-488, headpiece
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO Lec 3.2.8.1 / References: UniProt: Q17R67, UniProt: P08514*PLUS
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 50969.664 Da / Num. of mol.: 3 / Fragment: UNP residues 27-487
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 , 3 types, 11 molecules

#3: 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.: 2
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
#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
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 325 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 4.66 Å3/Da / Density % sol: 73.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 8000, 0.4 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 7.0, 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 QUANTUM 210 / 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: 122126 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 17.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 6 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 3 / Rsym value: 0.602 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDR

2vdr


Resolution: 2.9→44.59 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 20.427 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.447 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19741 3098 2.6 %RANDOM
Rwork0.17373 ---
obs0.17436 115380 95.21 %-
all-118478 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.195 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.254 Å / Luzzati sigma a free: 0.189 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20990 0 323 298 21611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02221878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214771
X-RAY DIFFRACTIONr_angle_refined_deg0.6571.97629791
X-RAY DIFFRACTIONr_angle_other_deg0.6453.00435772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54152726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40724.123992
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.696153425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5715143
X-RAY DIFFRACTIONr_chiral_restr0.0490.23301
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02124519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024399
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_it2.238813556
X-RAY DIFFRACTIONr_mcbond_other0.36185536
X-RAY DIFFRACTIONr_mcangle_it3.8871621825
X-RAY DIFFRACTIONr_scbond_it2.53688322
X-RAY DIFFRACTIONr_scangle_it4.194167964
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
1A2483MEDIUM POSITIONAL0.280.5
1C2483MEDIUM POSITIONAL0.20.5
1E2483MEDIUM POSITIONAL0.220.5
1A197LOOSE POSITIONAL0.35
1C197LOOSE POSITIONAL0.255
1E197LOOSE POSITIONAL0.335
1A2483MEDIUM THERMAL0.32
1C2483MEDIUM THERMAL0.32
1E2483MEDIUM THERMAL0.312
1A197LOOSE THERMAL0.1910
1C197LOOSE THERMAL0.210
1E197LOOSE THERMAL0.1910
2A280MEDIUM POSITIONAL0.110.5
2C280MEDIUM POSITIONAL0.080.5
2E280MEDIUM POSITIONAL0.10.5
2A329LOOSE POSITIONAL0.155
2C329LOOSE POSITIONAL0.135
2E329LOOSE POSITIONAL0.165
2A280MEDIUM THERMAL0.322
2C280MEDIUM THERMAL0.272
2E280MEDIUM THERMAL0.322
2A329LOOSE THERMAL0.2510
2C329LOOSE THERMAL0.2710
2E329LOOSE THERMAL0.2310
3A994MEDIUM POSITIONAL0.090.5
3C994MEDIUM POSITIONAL0.090.5
3E994MEDIUM POSITIONAL0.090.5
3A1164LOOSE POSITIONAL0.175
3C1164LOOSE POSITIONAL0.135
3E1164LOOSE POSITIONAL0.155
3A994MEDIUM THERMAL0.272
3C994MEDIUM THERMAL0.222
3E994MEDIUM THERMAL0.262
3A1164LOOSE THERMAL0.1810
3C1164LOOSE THERMAL0.1910
3E1164LOOSE THERMAL0.1710
4A316MEDIUM POSITIONAL0.170.5
4C316MEDIUM POSITIONAL0.110.5
4E316MEDIUM POSITIONAL0.120.5
4A362LOOSE POSITIONAL0.315
4C362LOOSE POSITIONAL0.25
4E362LOOSE POSITIONAL0.25
4A316MEDIUM THERMAL0.162
4C316MEDIUM THERMAL0.172
4E316MEDIUM THERMAL0.142
4A362LOOSE THERMAL0.1510
4C362LOOSE THERMAL0.1410
4E362LOOSE THERMAL0.110
5B744MEDIUM POSITIONAL0.110.5
5D744MEDIUM POSITIONAL0.090.5
5F744MEDIUM POSITIONAL0.090.5
5B958LOOSE POSITIONAL0.25
5D958LOOSE POSITIONAL0.215
5F958LOOSE POSITIONAL0.165
5B744MEDIUM THERMAL0.132
5D744MEDIUM THERMAL0.132
5F744MEDIUM THERMAL0.112
5B958LOOSE THERMAL0.110
5D958LOOSE THERMAL0.1110
5F958LOOSE THERMAL0.1110
6B1438MEDIUM POSITIONAL0.090.5
6D1438MEDIUM POSITIONAL0.10.5
6F1438MEDIUM POSITIONAL0.090.5
6B1765LOOSE POSITIONAL0.185
6D1765LOOSE POSITIONAL0.25
6F1765LOOSE POSITIONAL0.215
6B1438MEDIUM THERMAL0.232
6D1438MEDIUM THERMAL0.242
6F1438MEDIUM THERMAL0.212
6B1765LOOSE THERMAL0.2110
6D1765LOOSE THERMAL0.2110
6F1765LOOSE THERMAL0.1810
7B146MEDIUM POSITIONAL0.160.5
7D146MEDIUM POSITIONAL0.210.5
7F146MEDIUM POSITIONAL0.310.5
7B169LOOSE POSITIONAL0.185
7D169LOOSE POSITIONAL0.265
7F169LOOSE POSITIONAL0.35
7B146MEDIUM THERMAL0.072
7D146MEDIUM THERMAL0.072
7F146MEDIUM THERMAL0.072
7B169LOOSE THERMAL0.0610
7D169LOOSE THERMAL0.0610
7F169LOOSE THERMAL0.0710
LS refinement shellResolution: 2.9→2.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 168 -
Rwork0.279 7316 -
obs--82.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.876-0.1752-0.26041.3721-0.19921.13530.12650.12650.1198-0.1923-0.0026-0.0685-0.24830.0441-0.12380.2822-0.05590.0378-0.23730.061-0.145413.9738329.142123.9453
20.6219-0.20960.00591.87980.19520.65750.0537-0.0875-0.03560.14760.0227-0.3297-0.03080.1241-0.0764-0.02610.0074-0.0993-0.1747-0.0222-0.010639.2886287.59983.5237
30.45980.00330.11131.0875-0.24411.19190.02330.0783-0.02490.06380.0047-0.0714-0.20250.1037-0.02790.0667-0.12340.0584-0.2194-0.0688-0.105537.5458325.6202-24.0282
41.3412-0.2006-0.79590.7866-0.07621.3272-0.040.2563-0.1429-0.07940.09310.3786-0.1794-0.288-0.05320.08550.04890.0123-0.23210.11350.0215-12.5815319.321542.2503
51.31890.48690.05252.78120.50710.77990.1357-0.0156-0.21190.0681-0.11270.36160.06710.0217-0.023-0.06930.0291-0.1137-0.3404-0.01540.041917.5248263.6294-5.7713
61.1280.1304-0.39561.5608-0.05350.8102-0.02280.2596-0.0157-0.23620.0044-0.515-0.06340.54220.01840.0314-0.18710.1770.2489-0.07670.148263.1314323.1791-45.8958
79.4402-3.03554.33723.0206-2.02924.4383-0.2892-0.595-0.4398-0.17280.39250.18490.0005-0.2695-0.1033-0.08230.30060.1142-0.34210.3276-0.069-53.6462340.417440.5821
82.2114-2.36391.96269.252-5.32075.5579-0.1655-0.73290.223-0.2590.29451.0265-0.22270.0992-0.129-0.34770.2519-0.0444-0.4243-0.0140.023123.8454218.65864.5529
99.12264.28843.86535.24923.16014.1269-0.52390.8234-0.7580.35850.5835-0.91640.4717-0.29-0.0596-0.0772-0.20660.1814-0.17120.02950.4928101.4461349.0582-42.0582
107.0648-1.5707-2.22159.60040.29238.0763-0.3055-0.852-0.58060.31560.29120.83780.0077-0.89670.0143-0.18120.3090.0510.01740.4855-0.1037-81.3268357.511733.8367
119.21232.7962-2.31868.5314-0.97734.76460.6355-0.7509-1.2360.037-0.0649-0.0280.3084-0.1036-0.5706-0.41430.28-0.073-0.18050.3151-0.182832.3707188.481915.2911
126.3492-0.6601-0.75034.74082.16127.94420.0817-0.2841-0.49250.30040.5713-1.5356-0.10091.7743-0.653-0.38350.0106-0.11120.0163-0.1681.0591126.9953368.4969-33.9701
133.84572.04242.33139.0251-0.81411.94360.1520.38220.14170.0106-0.3310.68090.325-0.41760.1790.13440.07010.04670.3462-0.03680.2872-92.9542345.974226.4548
145.809-3.8696-0.41556.3359-6.23511.3125-0.0432-0.2513-0.35650.6283-0.11770.07760.0198-0.35710.1608-0.0283-0.088-0.02230.1720.05320.046321.8413182.727228.6945
150.28951.1824-0.2774.8293-1.13150.26510.9178-0.97690.46180.5165-1.1181-0.36610.43290.35850.20030.48650.2384-0.32681.11060.12671.5366139.4097358.7966-25.3761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 452
2X-RAY DIFFRACTION1A2004 - 2006
3X-RAY DIFFRACTION2C1 - 452
4X-RAY DIFFRACTION2C2004 - 2006
5X-RAY DIFFRACTION3E1 - 452
6X-RAY DIFFRACTION3E2004 - 2006
7X-RAY DIFFRACTION4B109 - 352
8X-RAY DIFFRACTION4B2001 - 2003
9X-RAY DIFFRACTION5D109 - 352
10X-RAY DIFFRACTION5D2001 - 2003
11X-RAY DIFFRACTION6F109 - 352
12X-RAY DIFFRACTION6F2001 - 2003
13X-RAY DIFFRACTION7B58 - 108
14X-RAY DIFFRACTION7B353 - 433
15X-RAY DIFFRACTION8D58 - 108
16X-RAY DIFFRACTION8D353 - 433
17X-RAY DIFFRACTION9F58 - 108
18X-RAY DIFFRACTION9F353 - 433
19X-RAY DIFFRACTION10B1 - 57
20X-RAY DIFFRACTION10B434 - 436
21X-RAY DIFFRACTION11D1 - 57
22X-RAY DIFFRACTION11D434 - 436
23X-RAY DIFFRACTION12F1 - 57
24X-RAY DIFFRACTION12F434 - 436
25X-RAY DIFFRACTION13B437 - 461
26X-RAY DIFFRACTION14D437 - 461
27X-RAY DIFFRACTION15F437 - 461

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