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- PDB-4ch8: High-salt crystal structure of a thrombin-GpIbalpha peptide complex -

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Basic information

Entry
Database: PDB / ID: 4ch8
TitleHigh-salt crystal structure of a thrombin-GpIbalpha peptide complex
Components
  • PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
  • THROMBIN, HEAVY CHAIN
  • THROMBIN, LIGHT CHAIN
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / COMPLEX
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / release of sequestered calcium ion into cytosol / negative regulation of cytokine production involved in inflammatory response / extracellular matrix / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : ...Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Kringle-like fold / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLechtenberg, B.C. / Freund, S.M.V. / Huntington, J.A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Gpibalpha Interacts Exclusively with Exosite II of Thrombin
Authors: Lechtenberg, B.C. / Freund, S.M.V. / Huntington, J.A.
History
DepositionNov 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references / Derived calculations / Other
Revision 1.2Dec 25, 2013Group: Non-polymer description
Revision 1.3Feb 12, 2014Group: Database references
Revision 1.4Jun 27, 2018Group: Advisory / Data collection / Structure summary / Category: pdbx_molecule / pdbx_unobs_or_zero_occ_atoms
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THROMBIN, LIGHT CHAIN
B: THROMBIN, HEAVY CHAIN
C: THROMBIN, LIGHT CHAIN
D: THROMBIN, HEAVY CHAIN
E: THROMBIN, LIGHT CHAIN
F: THROMBIN, HEAVY CHAIN
G: THROMBIN, LIGHT CHAIN
H: THROMBIN, HEAVY CHAIN
P: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
Q: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
R: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
S: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,34122
Polymers143,24912
Non-polymers2,09210
Water7,638424
1
A: THROMBIN, LIGHT CHAIN
B: THROMBIN, HEAVY CHAIN
P: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3816
Polymers35,8123
Non-polymers5693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-13.5 kcal/mol
Surface area14110 Å2
MethodPQS
2
C: THROMBIN, LIGHT CHAIN
D: THROMBIN, HEAVY CHAIN
Q: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2895
Polymers35,8123
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-9.8 kcal/mol
Surface area14580 Å2
MethodPQS
3
E: THROMBIN, LIGHT CHAIN
F: THROMBIN, HEAVY CHAIN
R: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3816
Polymers35,8123
Non-polymers5693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-7.9 kcal/mol
Surface area14500 Å2
MethodPQS
4
G: THROMBIN, LIGHT CHAIN
H: THROMBIN, HEAVY CHAIN
S: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2895
Polymers35,8123
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-6.9 kcal/mol
Surface area14860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.220, 51.330, 150.080
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYRAA292 - 3168 - 32
21ASPASPTYRTYRCC292 - 3168 - 32
12ASPASPSERSERAA292 - 3158 - 31
22ASPASPSERSEREE292 - 3158 - 31
13ASPASPTYRTYRAA292 - 3168 - 32
23ASPASPTYRTYRGG292 - 3168 - 32
14ILEILEGLNGLNBB321 - 5761 - 256
24ILEILEGLNGLNDD321 - 5761 - 256
15ILEILEPHEPHEBB321 - 5771 - 257
25ILEILEPHEPHEFF321 - 5771 - 257
16ILEILEPHEPHEBB321 - 5771 - 257
26ILEILEPHEPHEHH321 - 5771 - 257
17ALAALASERSERCC291 - 3157 - 31
27ALAALASERSEREE291 - 3157 - 31
18ASPASPILEILECC292 - 3178 - 33
28ASPASPILEILEGG292 - 3178 - 33
19ILEILEPHEPHEDD321 - 5771 - 257
29ILEILEPHEPHEFF321 - 5771 - 257
110ILEILEGLUGLUDD321 - 5791 - 259
210ILEILEGLUGLUHH321 - 5791 - 259
111ASPASPSERSEREE292 - 3158 - 31
211ASPASPSERSERGG292 - 3158 - 31
112ILEILEPHEPHEFF321 - 5771 - 257
212ILEILEPHEPHEHH321 - 5771 - 257

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

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Components

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Protein/peptide , 2 types, 8 molecules ACEGPQRS

#1: Protein/peptide
THROMBIN, LIGHT CHAIN / COAGULATION FACTOR II


Mass: 4096.534 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin
#3: Protein/peptide
PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300 / GP-IB ALPHA / GPIB-ALPHA / GPIBA / GLYCOPROTEIN IBALPHA / ANTIGEN CD42B-ALPHA / GPIBALPHA PEPTIDE


Mass: 1935.584 Da / Num. of mol.: 4
Fragment: C-TERMINAL FRAGMENT OF GPIBALPHA, RESIDUES 271-284
Source method: obtained synthetically / Details: ALL THREE TYROSINE RESIDUES ARE PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07359

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Protein , 1 types, 4 molecules BDFH

#2: Protein
THROMBIN, HEAVY CHAIN


Mass: 29780.219 Da / Num. of mol.: 4 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin

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Non-polymers , 4 types, 434 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsDEOXY-CHLOROMETHYL-ARGININE (ACL): MODIFIED BY REACTION WITH ACTIVE SITE HIS AND SER.

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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: 2.18 Å3/Da / Density % sol: 43.55 % / Description: NONE
Crystal growpH: 7.4 / Details: 100 MM SODIUM FORMATE, 18% PEG-3350, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.75→43.45 Å / Num. obs: 105859 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPB

1ppb


Resolution: 1.75→42.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.849 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24235 5305 5 %RANDOM
Rwork0.20955 ---
obs0.21122 100531 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.404 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.54 Å2
2--1.86 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8928 0 136 424 9488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199361
X-RAY DIFFRACTIONr_bond_other_d0.0090.028751
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.97612700
X-RAY DIFFRACTIONr_angle_other_deg1.4093.00320053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97851144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48523.531405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74151526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2631565
X-RAY DIFFRACTIONr_chiral_restr0.1150.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110470
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022153
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A8530.12
12C8530.12
21A8120.12
22E8120.12
31A8380.13
32G8380.13
41B151770.09
42D151770.09
51B147050.09
52F147050.09
61B149030.09
62H149030.09
71C10980.1
72E10980.1
81C11730.15
82G11730.15
91D147480.08
92F147480.08
101D151820.08
102H151820.08
111E9910.09
112G9910.09
121F147050.09
122H147050.09
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 364 -
Rwork0.362 7607 -
obs--95.74 %
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)
112.1436-5.21153.4144.59120.73353.03110.16461.71810.0072-0.1616-0.24980.015-0.04980.86560.08530.12890.04410.00350.6628-0.12810.133624.7713-13.614940.7962
26.17064.13816.88172.87264.54277.765-0.29860.65470.2209-0.16240.14740.1882-0.2950.91940.15120.2331-0.1071-0.00480.98820.01180.21922.4792-3.609137.6417
36.71998.98419.526412.651113.765715.1719-1.29051.4871-1.0009-1.67171.7993-0.7426-1.73791.7189-0.50880.258-0.30040.26010.8676-0.0251.006330.05793.780642.0265
42.8657-0.460.68120.0811-0.16590.827600.0106-0.14260.0060.01710.01930.1417-0.1379-0.01710.1921-0.0296-0.03830.06450.01450.225915.1653-11.404961.1289
55.37523.06521.62882.07671.59851.8686-0.13990.5222-0.66470.013-0.0178-0.19170.1773-0.53080.15760.1995-0.1451-0.04710.4083-0.19450.344710.0261-19.163153.1768
63.2125-0.34080.35290.2313-0.03980.9251-0.07830.3020.37150.031-0.0132-0.07520.04760.11280.09150.1473-0.027-0.05010.0430.05390.261725.1456-2.70358.0402
716.396-4.78133.3121.4024-0.72998.3079-0.25730.2444-0.72660.1369-0.06820.23431.86540.36670.32540.7718-0.1861-0.18170.27730.23690.5533-13.3853-15.769599.2825
87.3239-2.7897-3.37981.58620.38713.1317-0.551-1.0876-0.56570.11550.38370.27730.33720.5550.16730.32720.10510.01230.21470.1040.165-3.2913-13.7141111.3977
94.6664-3.81041.3494.5652-2.87664.2494-0.0105-0.3825-0.00740.31920.08270.0758-0.55980.3765-0.07220.27890.0061-0.03350.205-0.09940.1064-4.1021.241110.5242
100.9315-0.4994-0.77640.5255-0.18212.108-0.0761-0.0855-0.0049-0.0919-0.0967-0.040.28090.38270.17290.22350.0576-0.01730.09220.02560.22154.5324-11.066388.085
111.1829-0.4793-0.57660.4932-0.41141.9116-0.0194-0.13420.0893-0.0015-0.0215-0.0234-0.0870.16530.04090.19440.0146-0.03780.05-0.02960.2074-0.6078-3.686193.0632
121.78631.54690.03089.45023.92822.0875-0.00540.3232-0.07080.0024-0.11770.1761-0.0057-0.38030.12310.1741-0.0219-0.04360.2622-0.02010.2047-14.2622-11.530285.2593
1325.336-11.67948.79636.8429-7.53411.3852-0.24370.3821-1.0361-0.1045-0.13180.16680.41620.20650.37550.3069-0.10480.12550.5299-0.13970.199617.8236-37.4279117.5359
140.41460.77011.5011.94421.60758.3052-0.09220.01140.0148-0.2305-0.1211-0.033-0.15750.16450.21330.3334-0.06750.01250.30450.00440.091712.5535-29.2296112.0031
1513.7028.2711.47159.59351.379420.90560.68330.9529-0.5472-0.21340.26560.38080.42181.9163-0.94890.5933-0.0851-0.07540.25790.01280.264520.889-19.366116.4036
160.40360.1487-0.29081.05580.10632.0105-0.1588-0.059-0.0409-0.09580.0873-0.03250.1795-0.03190.07150.2088-0.0418-0.00850.0860.01570.167210.2998-33.8483133.412
174.0993-3.3509-2.77182.87632.36561.94690.07590.0351-0.04370.0097-0.0698-0.01540.0002-0.0533-0.00610.2510.0616-0.07990.14720.07660.2108-3.8571-16.3164132.3684
180.34710.126-0.17080.9842-0.02061.1916-0.1442-0.01230.0191-0.1630.1457-0.1151-0.15970.17-0.00150.209-0.0688-0.01150.1081-0.01050.196617.4442-22.3101132.0836
192.030.2232-0.00530.52810.99183.6981-0.1680.3685-0.18780.07680.0194-0.2310.1386-0.50450.14860.20.0008-0.01310.2485-0.1710.2903-20.1127-14.2134114.553
205.32592.417-1.00014.6753-2.3711.21650.29810.8971-0.09640.2277-0.17750.1687-0.10420.1129-0.12060.1950.1517-0.05960.6055-0.03070.0677-24.9777-2.3112112.7612
218.9574-1.4795.16352.13630.0463.4041-0.18690.5104-0.1127-0.22630.2703-0.02-0.2470.4519-0.08340.36910.11120.02610.22740.0080.0563-17.92914.3987111.8708
220.8679-0.1136-0.90070.2250.30611.658-0.01310.1318-0.09820.0874-0.12740.04290.0695-0.16280.14050.2002-0.016-0.00820.112-0.05370.1763-25.1544-10.6717135.5268
231.0825-0.0484-1.0070.66320.41512.00910.26040.4074-0.0066-0.0701-0.1203-0.006-0.4975-0.6818-0.14010.2390.17930.00150.24020.02960.1058-29.54893.4313128.3916
240.8371-0.1396-1.10890.1832-0.13962.24420.21120.20730.00320.0087-0.1046-0.0154-0.3598-0.1236-0.10660.24880.03910.00570.1087-0.00320.154-20.6931.3115130.3238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A292 - 302
2X-RAY DIFFRACTION2A303 - 310
3X-RAY DIFFRACTION3A311 - 317
4X-RAY DIFFRACTION4B321 - 384
5X-RAY DIFFRACTION5B385 - 403
6X-RAY DIFFRACTION6B404 - 577
7X-RAY DIFFRACTION7C287 - 294
8X-RAY DIFFRACTION8C295 - 305
9X-RAY DIFFRACTION9C306 - 318
10X-RAY DIFFRACTION10D321 - 376
11X-RAY DIFFRACTION11D377 - 563
12X-RAY DIFFRACTION12D564 - 579
13X-RAY DIFFRACTION13E291 - 296
14X-RAY DIFFRACTION14E297 - 311
15X-RAY DIFFRACTION15E312 - 316
16X-RAY DIFFRACTION16F321 - 463
17X-RAY DIFFRACTION17F464 - 477
18X-RAY DIFFRACTION18F478 - 577
19X-RAY DIFFRACTION19G292 - 305
20X-RAY DIFFRACTION20G306 - 312
21X-RAY DIFFRACTION21G313 - 318
22X-RAY DIFFRACTION22H321 - 449
23X-RAY DIFFRACTION23H450 - 499
24X-RAY DIFFRACTION24H500 - 579

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