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Basic information

Entry
Database: PDB / ID: 3nid
TitleThe Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3 -Specific Antagonist That Does Not Induce Opening
Components
  • (Monoclonal antibody 10E5 ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3Integrin beta 3
KeywordsCELL ADHESION/BLOOD CLOTTING / Integrin / headpiece / alphaIIB / beta3 / 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 / 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 ...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 / 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 / glycinergic synapse / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / blood coagulation, fibrin clot formation / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / cell-substrate junction assembly / mesodermal cell differentiation / angiogenesis involved in wound healing / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of postsynaptic neurotransmitter receptor internalization / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / wound healing, spreading of epidermal cells / apoptotic cell clearance / heterotypic cell-cell adhesion / positive regulation of cell adhesion mediated by integrin / integrin complex / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / positive regulation of leukocyte migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / smooth muscle cell migration / microvillus membrane / Syndecan interactions / negative chemotaxis / p130Cas linkage to MAPK signaling for integrins / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / activation of protein kinase activity / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / positive regulation of endothelial cell migration / protein kinase C binding / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / wound healing / cell-cell adhesion / platelet aggregation / platelet activation / ruffle membrane / VEGFA-VEGFR2 Pathway / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 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
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, J.H. / Zhu, J.Q. / Springer, T.A.
CitationJournal: Blood / Year: 2010
Title: Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening.
Authors: Zhu, J.H. / Zhu, J.Q. / Negri, A. / Provasi, D. / Filizola, M. / Coller, B.S. / Springer, T.A.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_unobs_or_zero_occ_atoms / 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.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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 heavy chain
F: Monoclonal antibody 10E5 light chain
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,25547
Polymers297,1488
Non-polymers5,10839
Water19,0781059
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,42425
Polymers148,5744
Non-polymers2,85021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 heavy chain
F: Monoclonal antibody 10E5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,83122
Polymers148,5744
Non-polymers2,25718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.970, 144.490, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23D
14B
24D
15B
25D
16H
26E
17H
27E
18L
28F
19L
29F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 454
2116C1 - 454
1126B1 - 57
2126D1 - 57
1146B109 - 352
2146D109 - 352
1156B433 - 466
2156D433 - 466
1166H1 - 119
2166E1 - 119
1176H120 - 221
2176E120 - 221
1186L1 - 108
2186F1 - 108
1196L109 - 214
2196F109 - 214

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Integrin alpha-IIb / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / Integrin alpha-IIb heavy chain


Mass: 49515.965 Da / Num. of mol.: 2 / Fragment: Integrin alpha-IIb, residues 32-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / Cell line (production host): Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08514
#2: Protein Integrin beta-3 / Integrin beta 3 / Platelet membrane glycoprotein IIIa / GPIIIa / CD61


Mass: 51958.789 Da / Num. of mol.: 2 / Fragment: Integrin beta-3, residues 27-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Plasmid: pCDNA 3.1, pEF1 / Cell (production host): CHO / Cell line (production host): Lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

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Antibody , 2 types, 4 molecules EHFL

#3: Antibody Monoclonal antibody 10E5 heavy chain


Mass: 23766.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA
#4: Antibody Monoclonal antibody 10E5 light chain


Mass: 23332.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 10E5 HYBRIDOMA

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Sugars , 4 types, 6 molecules

#5: 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
#6: 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.: 2
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
#7: 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
#12: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 5 types, 1092 molecules

#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00695 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2008
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00695 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 173699 / Num. obs: 169848 / % possible obs: 97.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.01 / Rsym value: 0.01 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.839 / % possible all: 96.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VDR

2vdr


Resolution: 2.3→48.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.963 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21474 1029 0.6 %RANDOM
Rwork0.17929 ---
obs0.1795 168819 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.822 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20715 0 302 1059 22076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02221579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214427
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.97129409
X-RAY DIFFRACTIONr_angle_other_deg0.783.00435078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71352712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89724.355930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.463153360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19115112
X-RAY DIFFRACTIONr_chiral_restr0.0670.23263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024269
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_it1.845513454
X-RAY DIFFRACTIONr_mcbond_other0.39155484
X-RAY DIFFRACTIONr_mcangle_it3.3271021723
X-RAY DIFFRACTIONr_scbond_it6.419208125
X-RAY DIFFRACTIONr_scangle_it8.437207676
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
1A5857LOOSE POSITIONAL0.310
1A5857LOOSE THERMAL3.1520
2B719LOOSE POSITIONAL0.5110
2B719LOOSE THERMAL2.8220
3B1651LOOSE POSITIONAL0.4410
3B1651LOOSE THERMAL2.7420
4B3151LOOSE POSITIONAL0.2610
4B3151LOOSE THERMAL2.7520
5B418LOOSE POSITIONAL0.5510
5B418LOOSE THERMAL2.9620
6H1555LOOSE POSITIONAL0.2710
6H1555LOOSE THERMAL2.0520
7H1166LOOSE POSITIONAL0.4310
7H1166LOOSE THERMAL2.1120
8L1358LOOSE POSITIONAL0.2210
8L1358LOOSE THERMAL2.1820
9L1388LOOSE POSITIONAL0.6110
9L1388LOOSE THERMAL3.8520
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 87 -
Rwork0.243 12241 -
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)
13.1594-1.2771-1.17322.82551.02272.37990.02980.22770.0685-0.2728-0.09250.3246-0.0798-0.38070.06270.11150.0063-0.01880.0930.02080.097345.5391.15638.829
21.7983-0.1062-0.02370.87450.38160.9889-0.0151-0.0601-0.02270.1712-0.0750.2380.099-0.2620.09020.1108-0.01290.07150.07930.00280.122242.00295.48362.63
31.12720.563-0.22734.3203-0.01882.02670.0052-0.1472-0.13640.28390.0395-0.43130.16640.1514-0.04470.12070.0523-0.00280.04720.02510.089466.48286.11260.393
41.52880.14750.23452.40860.44491.6093-0.05050.0057-0.13650.08780.0957-0.14480.13340.0865-0.04520.10860.03550.04820.01630.01440.071462.67582.83145.052
57.30653.4987-0.56187.99840.542920.4155-0.4309-0.4759-1.39490.31530.0177-0.46211.89490.8260.41320.55130.4608-0.00020.8971-0.12730.6934117.74984.85437.138
69.8713-1.1401-2.82083.97841.5987.4353-0.184-0.23160.52210.120.9776-1.56180.46013.2698-0.79360.32020.3624-0.07372.0489-0.3760.9612126.51491.02134.437
75.4651-4.2968-4.04267.57027.19968.61670.1963-0.12140.8312-0.29650.6433-0.5552-0.35031.0157-0.83960.1523-0.05770.03730.6441-0.18970.6635103.718113.18551.674
84.00131.4921-0.07282.71390.57561.41190.0367-0.34980.31140.12240.015-0.1198-0.22150.0491-0.05170.18680.02640.03960.0487-0.0160.144366.376123.02966.223
90.93790.69050.26292.5530.77151.3835-0.0153-0.03130.1056-0.01350.1094-0.1932-0.1230.1081-0.09410.10340.00960.0430.022-0.00280.121668.671116.07261.92
105.6166-0.98351.08375.91183.034314.1401-0.2167-0.2775-0.02520.67460.2820.18670.82290.9027-0.06530.19340.08540.0480.2895-0.02160.44798.881101.71857.386
113.7586-2.5965-3.33033.64324.73989.3908-0.11810.0651-0.14980.21470.16590.06280.32050.4981-0.04780.14030.0233-0.02220.4096-0.06480.450499.308104.78650.806
128.9120.83850.28881.5651-1.022415.0908-0.20170.27110.2249-0.24920.4248-0.24080.24361.1079-0.22310.23020.16060.09070.7523-0.02870.5872115.99788.54319.206
133.41220.6674-0.78071.8398-0.59983.2922-0.049-0.39990.11880.1329-0.0347-0.2733-0.0960.59390.08380.0877-0.01360.02110.3573-0.07190.131388.80695.168130.208
141.95010.55610.00461.1475-0.0871.2238-0.06810.117-0.0402-0.20080.0095-0.24010.17490.50020.05860.14940.0380.11050.2888-0.00220.119291.96189.763106.678
152.9155-1.89930.07323.7696-0.62023.3858-0.07510.0883-0.5233-0.14090.01890.18010.5204-0.03890.05620.2253-0.03520.05920.0386-0.01710.129671.22875.833114.608
162.73480.24850.13881.8903-0.11582.4722-0.0253-0.2804-0.3915-0.01380.0276-0.08610.43290.1906-0.00230.18490.04270.0620.15820.03560.086575.33680.371129.41
177.2185-2.174-3.358911.11725.586514.8679-0.21060.0546-1.16130.1127-0.3101-0.27091.7333-0.21250.52060.6905-0.33490.09180.51960.03860.475321.90768.585139.408
184.1918-1.1716-4.54256.1559-1.946416.0777-0.40130.2205-0.1430.2550.26961.04021.1969-2.26180.13170.3918-0.47410.07320.9015-0.03740.579911.20671.557140.351
192.40132.1587-2.90666.4555-7.285415.75560.2520.21540.27590.41520.260.26-0.8639-0.8008-0.5120.11760.02190.0360.4740.02640.229726.50995.776113.446
201.27410.144-0.27950.8109-0.56152.2242-0.04090.35080.2523-0.05950.06470.0714-0.0198-0.3251-0.02380.1994-0.02620.0350.15840.02680.099554.317100.93298.911
212.052-0.34630.73350.9116-0.2512.5049-0.06370.03030.243-0.05360.05270.0221-0.1443-0.16030.0110.1586-0.02320.0470.08050.01770.070460.754100.615101.18
224.17740.05990.79323.0294-0.792314.153-0.16120.1808-0.4332-0.2711-0.0301-0.17541.06890.0750.19130.1935-0.05450.08290.21310.03410.239136.181.49112.557
231.37540.348-1.55331.5444-1.819410.7579-0.1497-0.0034-0.1563-0.0377-0.0123-0.13070.5029-0.38520.1620.1375-0.07890.01540.27990.02150.193433.22886.016119.299
2413.61342.1181-1.04346.31514.79145.7472-0.0621-0.5614-0.24570.1347-0.16480.23390.4225-0.48360.2270.2066-0.14220.08180.1992-0.01370.218521.25679.357155.424
257.0473-3.9841-1.75717.0426-1.84136.3586-0.14890.504-1.0838-1.2615-0.281-0.10461.8576-0.01930.42990.8949-0.09160.23360.658-0.17930.4725115.55583.41686.172
265.5617-1.54632.58366.02020.67923.56780.24240.56470.3448-0.8975-0.3096-0.34490.35330.24150.06720.4977-0.0330.28220.60270.02210.2677114.53996.07985.703
275.0754-1.6493-1.14142.06590.27775.10730.19180.558-0.2263-1.1457-0.1956-0.28780.69340.05860.00380.8965-0.04030.30390.5976-0.04760.4264114.83789.88487.168
2813.1808-0.93361.3472.34313.27785.98080.46941.4765-0.57330.0201-0.1497-0.6087-0.28340.3701-0.31960.90880.04520.1180.69420.28671.1397149.51986.40576.128
297.1384-3.5521-3.71115.92463.84143.37960.4233-0.5207-0.7275-0.5386-0.4339-1.12290.0858-0.59430.01061.1217-0.19270.30521.18260.35461.4926147.33580.24683.838
308.26372.716111.76266.87487.537319.2779-0.99760.56870.644-0.660.1354-0.5555-1.43910.44450.86220.4721-0.02070.40090.919-0.08881.0173143.4789.47978.292
319.953.25713.293510.24432.44911.4262-0.29940.4432-0.2461-0.96570.1153-1.05120.07420.23640.18411.21210.15680.51451.49390.32862.0502157.54679.01279.305
328.8368-2.02254.95897.3534-1.72914.0285-0.526-0.55822.37740.1594-0.4667-1.8319-0.26690.35160.99270.3135-0.13790.02731.0993-0.08331.3404130.309104.795101.409
336.3495-1.3387-0.26356.0006-1.53724.4816-0.2463-0.34720.21540.2289-0.2145-0.84490.07140.50010.46080.1326-0.0830.12280.6446-0.00540.5106122.63798.01104.468
347.3458-2.12043.76554.9615-2.20886.10760.11430.30310.1959-0.277-0.3825-0.99860.29750.83050.26810.2-0.05830.26270.58560.06210.5284125.00699.15197.284
354.7729-0.6448-1.67712.88932.783814.1616-0.05060.08350.1119-0.97910.0554-0.1527-0.43620.7617-0.00480.6052-0.0280.22470.80770.28271.1422153.53598.31582.219
365.3162-2.8918-3.20285.92354.98754.3775-0.10910.2323-0.1549-0.72470.0938-0.1504-0.4169-0.04130.01530.69770.00480.36171.12720.30561.2476149.28695.41580.712
371.39580.3513-0.05536.03-2.13010.7594-0.2207-0.38570.5428-1.0653-0.3512-1.68410.34690.06420.57191.0097-0.41040.47661.66190.35261.7196158.336104.90581.403
3844.143-21.925917.848813.6955-11.22439.21152.31920.565-0.6625-1.1311-1.17211.42260.95291.0966-1.14711.04560.02120.35251.4972-0.13571.0203166.30496.91570.807
398.4421-2.2063-4.40834.90742.59349.490.0006-0.6526-0.61411.3577-0.04810.12290.8025-0.42730.04750.723-0.08190.05730.48350.08360.277418.44290.47686.48
403.50581.23790.45475.84140.88784.7140.2772-0.36640.30540.7872-0.26690.24450.0234-0.2016-0.01030.2573-0.03890.12510.2711-0.07560.189618.621101.60779.302
413.42280.3805-1.40333.1673-0.36494.31510.1169-0.62940.10441.1309-0.16060.17370.1264-0.28410.04370.4876-0.06740.11750.3933-0.05410.26218.76596.45681.074
425.10890.8922-1.44392.19771.5517.8077-0.2221-1.024-1.6111-0.0861-0.11570.38330.36820.15690.33780.51390.1050.30210.42280.22781.1514-13.57786.39694.347
4312.02989.01995.296111.00248.60858.4779-0.46340.4561-1.63081.23590.6632-0.38021.97231.5274-0.19980.83670.48640.21351.0006-0.06681.8325-7.57578.80191.011
4415.96376.64497.69452.98291.679915.3038-0.31520.1509-0.0891-0.09650.01170.021-0.1250.4580.30340.12580.08480.22040.2331-0.0250.6491-9.64688.79389.426
458.51460.85625.61614.1876-0.016611.8299-0.6136-0.9507-2.24690.5743-0.17210.00022.8046-0.30330.78571.55380.16110.90880.63130.2282.2721-17.96975.98894.842
463.4143-3.0312-1.85676.33420.93991.17360.10341.0981-0.6141-0.0828-0.35661.6337-0.0641-0.80120.25330.11090.0983-0.00470.9721-0.41761.09590.90198.90962.983
475.0210.2183-0.02244.44760.67063.24070.01410.2329-0.2732-0.062-0.34740.60080.1106-0.68330.33340.0264-0.00650.05280.42-0.12790.351710.32394.15562.466
488.46613.81220.74846.3782.68913.69120.0996-0.1175-0.1480.3958-0.51780.85180.222-0.70330.41820.08230.01530.14640.4548-0.14190.38297.08797.17468.661
498.93690.0206-1.07533.20430.91420.3946-0.51040.6409-2.17630.50730.13940.35520.2171-0.07070.3710.2215-0.08830.31270.4457-0.18861.3103-20.54887.86685.618
504.2898-2.1659-0.99693.48063.64275.2664-0.09230.5072-0.8182-0.0632-0.05160.3048-0.3547-0.25890.14380.1286-0.00770.08930.4965-0.08560.7063-21.33795.74683.245
515.3016-1.518-3.61143.01252.70510.7474-0.38160.3285-0.93630.1765-0.03940.3482-0.0577-0.31910.42110.082-0.05110.10640.334-0.0380.7181-21.12594.22985.258
5276.2091120.085623.8164191.526234.22212.21544.0626-1.7034-3.49244.2853-3.5156-5.83074.45280.4618-0.5472.55650.04460.471.527-0.34870.9033-34.4591.15597.278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 73
2X-RAY DIFFRACTION2A74 - 274
3X-RAY DIFFRACTION3A275 - 334
4X-RAY DIFFRACTION4A335 - 454
5X-RAY DIFFRACTION5B1 - 25
6X-RAY DIFFRACTION6B26 - 60
7X-RAY DIFFRACTION7B61 - 108
8X-RAY DIFFRACTION8B109 - 177
9X-RAY DIFFRACTION9B178 - 354
10X-RAY DIFFRACTION10B355 - 383
11X-RAY DIFFRACTION11B384 - 432
12X-RAY DIFFRACTION12B433 - 466
13X-RAY DIFFRACTION13C1 - 73
14X-RAY DIFFRACTION14C74 - 274
15X-RAY DIFFRACTION15C275 - 334
16X-RAY DIFFRACTION16C335 - 453
17X-RAY DIFFRACTION17D1 - 25
18X-RAY DIFFRACTION18D26 - 59
19X-RAY DIFFRACTION19D60 - 91
20X-RAY DIFFRACTION20D92 - 176
21X-RAY DIFFRACTION21D177 - 353
22X-RAY DIFFRACTION22D354 - 383
23X-RAY DIFFRACTION23D384 - 436
24X-RAY DIFFRACTION24D437 - 468
25X-RAY DIFFRACTION25E1 - 33
26X-RAY DIFFRACTION26E34 - 64
27X-RAY DIFFRACTION27E65 - 113
28X-RAY DIFFRACTION28E114 - 151
29X-RAY DIFFRACTION29E152 - 170
30X-RAY DIFFRACTION30E171 - 187
31X-RAY DIFFRACTION31E188 - 221
32X-RAY DIFFRACTION32F1 - 24
33X-RAY DIFFRACTION33F25 - 79
34X-RAY DIFFRACTION34F80 - 105
35X-RAY DIFFRACTION35F106 - 156
36X-RAY DIFFRACTION36F157 - 187
37X-RAY DIFFRACTION37F188 - 207
38X-RAY DIFFRACTION38F208 - 214
39X-RAY DIFFRACTION39H1 - 29
40X-RAY DIFFRACTION40H30 - 64
41X-RAY DIFFRACTION41H65 - 113
42X-RAY DIFFRACTION42H114 - 151
43X-RAY DIFFRACTION43H152 - 167
44X-RAY DIFFRACTION44H168 - 187
45X-RAY DIFFRACTION45H188 - 221
46X-RAY DIFFRACTION46L1 - 24
47X-RAY DIFFRACTION47L25 - 79
48X-RAY DIFFRACTION48L80 - 105
49X-RAY DIFFRACTION49L106 - 128
50X-RAY DIFFRACTION50L129 - 155
51X-RAY DIFFRACTION51L156 - 209
52X-RAY DIFFRACTION52L210 - 214

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