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- PDB-2v0t: The A178L mutation in the C-terminal hinge of the flexible loop-6... -

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Basic information

Entry
Database: PDB / ID: 2v0t
TitleThe A178L mutation in the C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (TIM) induces a more closed conformation of this hinge region in dimeric and monomeric TIM
ComponentsTRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
KeywordsISOMERASE / SOMERASE / TIM-BARREL
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytoplasm / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAlahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008
Title: Structural studies show that the A178L mutation in the C-terminal hinge of the catalytic loop-6 of triosephosphate isomerase (TIM) induces a closed-like conformation in dimeric and monomeric TIM.
Authors: Alahuhta, M. / Casteleijn, M.G. / Neubauer, P. / Wierenga, R.K.
History
DepositionMay 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
C: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
D: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
E: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
F: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
G: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
H: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,70120
Polymers215,2638
Non-polymers1,43712
Water26,4641469
1
A: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1045
Polymers53,8162
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-32.5 kcal/mol
Surface area23100 Å2
MethodPISA
2
C: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
E: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3426
Polymers53,8162
Non-polymers5264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-30.1 kcal/mol
Surface area23000 Å2
MethodPISA
3
D: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
F: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2465
Polymers53,8162
Non-polymers4303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-27.8 kcal/mol
Surface area23190 Å2
MethodPISA
4
G: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
H: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0084
Polymers53,8162
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25.3 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.690, 79.250, 174.000
Angle α, β, γ (deg.)90.00, 99.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEASNASN1BB7 - 117 - 11
21ILEILEASNASN1AA7 - 117 - 11
31ILEILEASNASN1CC7 - 117 - 11
41ILEILEASNASN1DD7 - 117 - 11
51ILEILEASNASN1EE7 - 117 - 11
61ILEILEASNASN1FF7 - 117 - 11
71ILEILEASNASN1GG7 - 117 - 11
81ILEILEASNASN1HH7 - 117 - 11
12SERSERSERSER3BB20 - 2220 - 22
22SERSERSERSER3AA20 - 2220 - 22
32SERSERSERSER3CC20 - 2220 - 22
42SERSERSERSER3DD20 - 2220 - 22
52SERSERSERSER3EE20 - 2220 - 22
62SERSERSERSER3FF20 - 2220 - 22
72SERSERSERSER3GG20 - 2220 - 22
82SERSERSERSER3HH20 - 2220 - 22
13GLNGLNALAALA1BB38 - 4238 - 42
23GLNGLNALAALA1AA38 - 4238 - 42
33GLNGLNALAALA1CC38 - 4238 - 42
43GLNGLNALAALA1DD38 - 4238 - 42
53GLNGLNALAALA1EE38 - 4238 - 42
63GLNGLNALAALA1FF38 - 4238 - 42
73GLNGLNALAALA1GG38 - 4238 - 42
83GLNGLNALAALA1HH38 - 4238 - 42
14HISHISLYSLYS3BB47 - 5247 - 52
24HISHISLYSLYS3AA47 - 5247 - 52
34HISHISLYSLYS3CC47 - 5247 - 52
44HISHISLYSLYS3DD47 - 5247 - 52
54HISHISLYSLYS3EE47 - 5247 - 52
64HISHISLYSLYS3FF47 - 5247 - 52
74HISHISLYSLYS3GG47 - 5247 - 52
84HISHISLYSLYS3HH47 - 5247 - 52
15VALVALALAALA1BB61 - 6461 - 64
25VALVALALAALA1AA61 - 6461 - 64
35VALVALALAALA1CC61 - 6461 - 64
45VALVALALAALA1DD61 - 6461 - 64
55VALVALALAALA1EE61 - 6461 - 64
65VALVALALAALA1FF61 - 6461 - 64
75VALVALALAALA1GG61 - 6461 - 64
85VALVALALAALA1HH61 - 6461 - 64
16SERSERGLYGLY3BB79 - 8779 - 87
26SERSERGLYGLY3AA79 - 8779 - 87
36SERSERGLYGLY3CC79 - 8779 - 87
46SERSERGLYGLY3DD79 - 8779 - 87
56SERSERGLYGLY3EE79 - 8779 - 87
66SERSERGLYGLY3FF79 - 8779 - 87
76SERSERGLYGLY3GG79 - 8779 - 87
86SERSERGLYGLY3HH79 - 8779 - 87
17TRPTRPLEULEU1BB90 - 9390 - 93
27TRPTRPLEULEU1AA90 - 9390 - 93
37TRPTRPLEULEU1CC90 - 9390 - 93
47TRPTRPLEULEU1DD90 - 9390 - 93
57TRPTRPLEULEU1EE90 - 9390 - 93
67TRPTRPLEULEU1FF90 - 9390 - 93
77TRPTRPLEULEU1GG90 - 9390 - 93
87TRPTRPLEULEU1HH90 - 9390 - 93
18THRTHRGLYGLY3BB105 - 120105 - 120
28THRTHRGLYGLY3AA105 - 120105 - 120
38THRTHRGLYGLY3CC105 - 120105 - 120
48THRTHRGLYGLY3DD105 - 120105 - 120
58THRTHRGLYGLY3EE105 - 120105 - 120
68THRTHRGLYGLY3FF105 - 120105 - 120
78THRTHRGLYGLY3GG105 - 120105 - 120
88THRTHRGLYGLY3HH105 - 120105 - 120
19METMETILEILE1BB122 - 127122 - 127
29METMETILEILE1AA122 - 127122 - 127
39METMETILEILE1CC122 - 127122 - 127
49METMETILEILE1DD122 - 127122 - 127
59METMETILEILE1EE122 - 127122 - 127
69METMETILEILE1FF122 - 127122 - 127
79METMETILEILE1GG122 - 127122 - 127
89METMETILEILE1HH122 - 127122 - 127
110ALAALAALAALA3BB140 - 151140 - 151
210ALAALAALAALA3AA140 - 151140 - 151
310ALAALAALAALA3CC140 - 151140 - 151
410ALAALAALAALA3DD140 - 151140 - 151
510ALAALAALAALA3EE140 - 151140 - 151
610ALAALAALAALA3FF140 - 151140 - 151
710ALAALAALAALA3GG140 - 151140 - 151
810ALAALAALAALA3HH140 - 151140 - 151
111VALVALTYRTYR1BB163 - 166163 - 166
211VALVALTYRTYR1AA163 - 166163 - 166
311VALVALTYRTYR1CC163 - 166163 - 166
411VALVALTYRTYR1DD163 - 166163 - 166
511VALVALTYRTYR1EE163 - 166163 - 166
611VALVALTYRTYR1FF163 - 166163 - 166
711VALVALTYRTYR1GG163 - 166163 - 166
811VALVALTYRTYR1HH163 - 166163 - 166
112ALAALASERSER3BB183 - 196183 - 196
212ALAALASERSER3AA183 - 196183 - 196
312ALAALASERSER3CC183 - 196183 - 196
412ALAALASERSER3DD183 - 196183 - 196
512ALAALASERSER3EE183 - 196183 - 196
612ALAALASERSER3FF183 - 196183 - 196
712ALAALASERSER3GG183 - 196183 - 196
812ALAALASERSER3HH183 - 196183 - 196
113ARGARGTYRTYR1BB207 - 210207 - 210
213ARGARGTYRTYR1AA207 - 210207 - 210
313ARGARGTYRTYR1CC207 - 210207 - 210
413ARGARGTYRTYR1DD207 - 210207 - 210
513ARGARGTYRTYR1EE207 - 210207 - 210
613ARGARGTYRTYR1FF207 - 210207 - 210
713ARGARGTYRTYR1GG207 - 210207 - 210
813ARGARGTYRTYR1HH207 - 210207 - 210
114THRTHRTYRTYR3BB221 - 223221 - 223
214THRTHRTYRTYR3AA221 - 223221 - 223
314THRTHRTYRTYR3CC221 - 223221 - 223
414THRTHRTYRTYR3DD221 - 223221 - 223
514THRTHRTYRTYR3EE221 - 223221 - 223
614THRTHRTYRTYR3FF221 - 223221 - 223
714THRTHRTYRTYR3GG221 - 223221 - 223
814THRTHRTYRTYR3HH221 - 223221 - 223
115GLYGLYVALVAL1BB230 - 233230 - 233
215GLYGLYVALVAL1AA230 - 233230 - 233
315GLYGLYVALVAL1CC230 - 233230 - 233
415GLYGLYVALVAL1DD230 - 233230 - 233
515GLYGLYVALVAL1EE230 - 233230 - 233
615GLYGLYVALVAL1FF230 - 233230 - 233
715GLYGLYVALVAL1GG230 - 233230 - 233
815GLYGLYVALVAL1HH230 - 233230 - 233
116GLUGLUTHRTHR3BB241 - 249241 - 249
216GLUGLUTHRTHR3AA241 - 249241 - 249
316GLUGLUTHRTHR3CC241 - 249241 - 249
416GLUGLUTHRTHR3DD241 - 249241 - 249
516GLUGLUTHRTHR3EE241 - 249241 - 249
616GLUGLUTHRTHR3FF241 - 249241 - 249
716GLUGLUTHRTHR3GG241 - 249241 - 249
816GLUGLUTHRTHR3HH241 - 249241 - 249
117LEULEUTHRTHR3BB24 - 3124 - 31
217LEULEUTHRTHR3AA24 - 3124 - 31
317LEULEUTHRTHR3CC24 - 3124 - 31
417LEULEUTHRTHR3DD24 - 3124 - 31
517LEULEUTHRTHR3EE24 - 3124 - 31
617LEULEUTHRTHR3FF24 - 3124 - 31
717LEULEUTHRTHR3GG24 - 3124 - 31
817LEULEUTHRTHR3HH24 - 3124 - 31

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL / TIM / TRIOSE- PHOSPHATE ISOMERASE


Mass: 26907.912 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): PLYSS / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1469 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN B, ALA 178 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN B, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN C, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN D, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN E, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN F, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN G, ALA 178 TO LEU ENGINEERED RESIDUE IN CHAIN H, ALA 178 TO LEU

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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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 8% ETHYLENE GLYCOL AND 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 2006 / Details: MONTEL MIRRORS
RadiationMonochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.22 Å / Num. obs: 103058 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ML1

1ml1


Resolution: 2.2→19.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.413 / SU ML: 0.172 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5153 5 %RANDOM
Rwork0.178 ---
obs0.181 97902 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.73 Å2
2--1.09 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14886 0 80 1469 16435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.94420670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69451949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65424.614609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.934152572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71572
X-RAY DIFFRACTIONr_chiral_restr0.1520.22404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.27502
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.210370
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.21281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.59912
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.964215583
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67936008
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.684.55087
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

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B586tight positional0.060.05
2A586tight positional0.060
3C586tight positional0.080
4D586tight positional0.050
5E586tight positional0.050
6F586tight positional0.050
7G586tight positional0.050
8H586tight positional0.050
1B269loose positional0.075
2A269loose positional0.060.02
3C269loose positional0.070
4D269loose positional0.060
5E269loose positional0.070
6F269loose positional0.060
7G269loose positional0.060
8H269loose positional0.060
1B586tight thermal0.150.5
2A586tight thermal0.140
3C586tight thermal0.140
4D586tight thermal0.130
5E586tight thermal0.150
6F586tight thermal0.130
7G586tight thermal0.110
8H586tight thermal0.120
1B269loose thermal0.1410
2A269loose thermal0.140.04
3C269loose thermal0.130
4D269loose thermal0.140
5E269loose thermal0.140
6F269loose thermal0.140
7G269loose thermal0.110
8H269loose thermal0.130
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 319 -
Rwork0.273 6057 -
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)
11.9575-0.09920.1790.86550.03711.14290.00690.06220.0327-0.08110.0071-0.1577-0.03590.1889-0.0141-0.11420.00020.0063-0.10520.0026-0.081749.5839.10389.945
22.16670.0325-0.25141.13120.08451.31490.0244-0.1640.02030.0802-0.01610.1621-0.0235-0.2085-0.0082-0.11840.0093-0.0047-0.08450.0209-0.097714.23538.85993.408
32.1280.2611-0.01461.24720.40770.769-0.0004-0.0441-0.16910.12250.02890.13860.1153-0.0732-0.0285-0.14960.004-0.0057-0.1222-0.0042-0.066541.20635.30811.784
41.8025-0.2760.45280.8974-0.10811.220.0083-0.14030.18040.08990.02490.1073-0.1272-0.1203-0.0333-0.0820.01010.0174-0.0906-0.0071-0.107921.4170.05933.792
52.01510.72150.40110.97750.21541.4064-0.0080.2544-0.1301-0.02020.0835-0.1674-0.09030.2136-0.0756-0.15630.0139-0.0107-0.0813-0.0579-0.066875.55642.7478.484
62.0678-0.5666-0.16010.97410.34911.1387-0.0065-0.21630.03540.11670.0387-0.1280.07870.1539-0.0322-0.0682-0.0046-0.0193-0.0628-0.03-0.11954.72860.44641.402
72.09581.01980.28381.41510.08891.2615-0.26610.41020.0242-0.21790.21230.1418-0.1255-0.11610.05390.0499-0.0625-0.04810.03790.0109-0.071158.97817.88647.932
82.39120.90860.55221.09220.69551.4513-0.23590.3273-0.0028-0.13410.1593-0.1684-0.14540.12570.07650.0872-0.104-0.0422-0.02140.0181-0.070891.02430.75555.223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 250
2X-RAY DIFFRACTION2B2 - 250
3X-RAY DIFFRACTION3C2 - 250
4X-RAY DIFFRACTION4D2 - 250
5X-RAY DIFFRACTION5E2 - 250
6X-RAY DIFFRACTION6F2 - 250
7X-RAY DIFFRACTION7G2 - 250
8X-RAY DIFFRACTION8H2 - 250

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