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- PDB-5us6: Structure of Dihydrodipicolinate Reductase from Vibrio vulnificus... -

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Basic information

Entry
Database: PDB / ID: 5us6
TitleStructure of Dihydrodipicolinate Reductase from Vibrio vulnificus Bound to NADH and 2,6 Pyridine Dicarboxylic Acid with Intact Polyhistidine Tag
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRIDINE-2,6-DICARBOXYLIC ACID / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.61 Å
AuthorsMank, N.M. / Arnette, A.K. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
C: 4-hydroxy-tetrahydrodipicolinate reductase
D: 4-hydroxy-tetrahydrodipicolinate reductase
E: 4-hydroxy-tetrahydrodipicolinate reductase
F: 4-hydroxy-tetrahydrodipicolinate reductase
G: 4-hydroxy-tetrahydrodipicolinate reductase
H: 4-hydroxy-tetrahydrodipicolinate reductase
I: 4-hydroxy-tetrahydrodipicolinate reductase
J: 4-hydroxy-tetrahydrodipicolinate reductase
K: 4-hydroxy-tetrahydrodipicolinate reductase
L: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,86453
Polymers377,17912
Non-polymers9,68441
Water2,900161
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
C: 4-hydroxy-tetrahydrodipicolinate reductase
D: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,98718
Polymers125,7264
Non-polymers3,26014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-117 kcal/mol
Surface area39440 Å2
MethodPISA
2
E: 4-hydroxy-tetrahydrodipicolinate reductase
F: 4-hydroxy-tetrahydrodipicolinate reductase
G: 4-hydroxy-tetrahydrodipicolinate reductase
H: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,08319
Polymers125,7264
Non-polymers3,35615
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-133 kcal/mol
Surface area39500 Å2
MethodPISA
3
I: 4-hydroxy-tetrahydrodipicolinate reductase
J: 4-hydroxy-tetrahydrodipicolinate reductase
K: 4-hydroxy-tetrahydrodipicolinate reductase
L: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,79416
Polymers125,7264
Non-polymers3,06812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16790 Å2
ΔGint-90 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.906, 115.845, 148.127
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 26426 - 289
21METMETLEULEUBB1 - 26426 - 289
12METMETGLYGLYAA1 - 26526 - 290
22METMETGLYGLYCC1 - 26526 - 290
13METMETASNASNAA1 - 26726 - 292
23METMETASNASNDD1 - 26726 - 292
14METMETASNASNAA1 - 26726 - 292
24METMETASNASNEE1 - 26726 - 292
15METMETLEULEUAA1 - 26426 - 289
25METMETLEULEUFF1 - 26426 - 289
16METMETGLYGLYAA1 - 26526 - 290
26METMETGLYGLYGG1 - 26526 - 290
17METMETASNASNAA1 - 26726 - 292
27METMETASNASNHH1 - 26726 - 292
18METMETASNASNAA1 - 26726 - 292
28METMETASNASNII1 - 26726 - 292
19METMETGLYGLYAA1 - 26526 - 290
29METMETGLYGLYJJ1 - 26526 - 290
110METMETGLYGLYAA1 - 26526 - 290
210METMETGLYGLYKK1 - 26526 - 290
111METMETASNASNAA1 - 26726 - 292
211METMETASNASNLL1 - 26726 - 292
112METMETLEULEUBB1 - 26426 - 289
212METMETLEULEUCC1 - 26426 - 289
113METMETGLYGLYBB1 - 26526 - 290
213METMETGLYGLYDD1 - 26526 - 290
114METMETLEULEUBB1 - 26426 - 289
214METMETLEULEUEE1 - 26426 - 289
115GLYGLYGLYGLYBB0 - 26525 - 290
215GLYGLYGLYGLYFF0 - 26525 - 290
116METMETLEULEUBB1 - 26426 - 289
216METMETLEULEUGG1 - 26426 - 289
117METMETGLYGLYBB1 - 26526 - 290
217METMETGLYGLYHH1 - 26526 - 290
118METMETLEULEUBB1 - 26426 - 289
218METMETLEULEUII1 - 26426 - 289
119GLYGLYLEULEUBB0 - 26425 - 289
219GLYGLYLEULEUJJ0 - 26425 - 289
120METMETLEULEUBB1 - 26426 - 289
220METMETLEULEUKK1 - 26426 - 289
121METMETGLYGLYBB1 - 26526 - 290
221METMETGLYGLYLL1 - 26526 - 290
122METMETLEULEUCC1 - 26626 - 291
222METMETLEULEUDD1 - 26626 - 291
123METMETGLYGLYCC1 - 26526 - 290
223METMETGLYGLYEE1 - 26526 - 290
124METMETLEULEUCC1 - 26426 - 289
224METMETLEULEUFF1 - 26426 - 289
125METMETLEULEUCC1 - 26626 - 291
225METMETLEULEUGG1 - 26626 - 291
126METMETLEULEUCC1 - 26626 - 291
226METMETLEULEUHH1 - 26626 - 291
127METMETGLYGLYCC1 - 26526 - 290
227METMETGLYGLYII1 - 26526 - 290
128METMETGLYGLYCC1 - 26526 - 290
228METMETGLYGLYJJ1 - 26526 - 290
129METMETLEULEUCC1 - 26626 - 291
229METMETLEULEUKK1 - 26626 - 291
130METMETLEULEUCC1 - 26626 - 291
230METMETLEULEULL1 - 26626 - 291
131METMETASNASNDD1 - 26726 - 292
231METMETASNASNEE1 - 26726 - 292
132METMETGLYGLYDD1 - 26526 - 290
232METMETGLYGLYFF1 - 26526 - 290
133METMETLEULEUDD1 - 26626 - 291
233METMETLEULEUGG1 - 26626 - 291
134METMETASNASNDD1 - 26726 - 292
234METMETASNASNHH1 - 26726 - 292
135METMETASNASNDD1 - 26726 - 292
235METMETASNASNII1 - 26726 - 292
136METMETLEULEUDD1 - 26626 - 291
236METMETLEULEUJJ1 - 26626 - 291
137METMETLEULEUDD1 - 26626 - 291
237METMETLEULEUKK1 - 26626 - 291
138METMETASNASNDD1 - 26726 - 292
238METMETASNASNLL1 - 26726 - 292
139METMETLEULEUEE1 - 26426 - 289
239METMETLEULEUFF1 - 26426 - 289
140METMETGLYGLYEE1 - 26526 - 290
240METMETGLYGLYGG1 - 26526 - 290
141METMETASNASNEE1 - 26726 - 292
241METMETASNASNHH1 - 26726 - 292
142METMETASNASNEE1 - 26726 - 292
242METMETASNASNII1 - 26726 - 292
143METMETGLYGLYEE1 - 26526 - 290
243METMETGLYGLYJJ1 - 26526 - 290
144METMETGLYGLYEE1 - 26526 - 290
244METMETGLYGLYKK1 - 26526 - 290
145METMETASNASNEE1 - 26726 - 292
245METMETASNASNLL1 - 26726 - 292
146METMETLEULEUFF1 - 26426 - 289
246METMETLEULEUGG1 - 26426 - 289
147METMETGLYGLYFF1 - 26526 - 290
247METMETGLYGLYHH1 - 26526 - 290
148METMETLEULEUFF1 - 26426 - 289
248METMETLEULEUII1 - 26426 - 289
149GLYGLYLEULEUFF0 - 26425 - 289
249GLYGLYLEULEUJJ0 - 26425 - 289
150METMETLEULEUFF1 - 26426 - 289
250METMETLEULEUKK1 - 26426 - 289
151METMETGLYGLYFF1 - 26526 - 290
251METMETGLYGLYLL1 - 26526 - 290
152METMETLEULEUGG1 - 26626 - 291
252METMETLEULEUHH1 - 26626 - 291
153METMETGLYGLYGG1 - 26526 - 290
253METMETGLYGLYII1 - 26526 - 290
154METMETGLYGLYGG1 - 26526 - 290
254METMETGLYGLYJJ1 - 26526 - 290
155METMETLEULEUGG1 - 26626 - 291
255METMETLEULEUKK1 - 26626 - 291
156METMETLEULEUGG1 - 26626 - 291
256METMETLEULEULL1 - 26626 - 291
157METMETASNASNHH1 - 26726 - 292
257METMETASNASNII1 - 26726 - 292
158METMETLEULEUHH1 - 26626 - 291
258METMETLEULEUJJ1 - 26626 - 291
159METMETLEULEUHH1 - 26626 - 291
259METMETLEULEUKK1 - 26626 - 291
160METMETASPASPHH1 - 26826 - 293
260METMETASPASPLL1 - 26826 - 293
161METMETGLYGLYII1 - 26526 - 290
261METMETGLYGLYJJ1 - 26526 - 290
162METMETGLYGLYII1 - 26526 - 290
262METMETGLYGLYKK1 - 26526 - 290
163METMETASNASNII1 - 26726 - 292
263METMETASNASNLL1 - 26726 - 292
164METMETGLYGLYJJ1 - 26526 - 290
264METMETGLYGLYKK1 - 26526 - 290
165METMETLEULEUJJ1 - 26626 - 291
265METMETLEULEULL1 - 26626 - 291
166METMETLEULEUKK1 - 26626 - 291
266METMETLEULEULL1 - 26626 - 291

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

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Components

#1: Protein
4-hydroxy-tetrahydrodipicolinate reductase / / HTPA reductase


Mass: 31431.605 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: dapB, VV1_0567 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DEM0, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID / Dipicolinic acid


Mass: 167.119 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.53 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.26 M ammonium sulfate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 106437 / % possible obs: 93.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Χ2: 1.52 / Net I/av σ(I): 20.236 / Net I/σ(I): 7 / Num. measured all: 326033
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.10.6420.8730.4040.760.91993
2.64-2.693.10.5550.9150.350.6580.93792.8
2.69-2.743.10.4740.9190.2980.5610.92892.6
2.74-2.83.10.3960.9380.250.470.96992.6
2.8-2.863.10.3390.9480.2140.4011.00592.9
2.86-2.933.10.2850.9660.180.3380.98592.7
2.93-33.10.2180.9780.1370.2581.06992.7
3-3.083.10.1880.9820.1190.2231.09792.8
3.08-3.173.10.1610.9850.1020.1911.18992.6
3.17-3.283.10.1310.9880.0830.1561.21492.8
3.28-3.393.10.1120.9910.0710.1331.33993.3
3.39-3.533.10.0960.9940.0610.1141.43193.9
3.53-3.6930.1020.9890.0680.1232.34391.2
3.69-3.8830.0880.9930.0570.1062.44993.9
3.88-4.132.90.0760.9940.050.0912.06594
4.13-4.443.10.0690.9950.0440.0822.1196.2
4.44-4.8930.0660.9940.0430.0792.16396.6
4.89-5.630.0660.9950.0430.0782.03895.7
5.6-7.053.10.0570.9970.0360.0681.78894.6
7.05-4030.0510.9950.0340.0622.4891.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.61→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 28.234 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 1.266 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25684 5512 5.2 %RANDOM
Rwork0.22756 ---
obs0.22907 100856 92.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.147 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å2-0 Å21.82 Å2
2---5.7 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.61→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23010 0 619 161 23790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01923990
X-RAY DIFFRACTIONr_bond_other_d00.0221985
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.97232631
X-RAY DIFFRACTIONr_angle_other_deg3.857350602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7853141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88724.615949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69153636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.69815120
X-RAY DIFFRACTIONr_chiral_restr0.0960.23836
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0227138
X-RAY DIFFRACTIONr_gen_planes_other0.010.024710
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_it2.6843.92112618
X-RAY DIFFRACTIONr_mcbond_other2.6823.92112617
X-RAY DIFFRACTIONr_mcangle_it4.3435.87215741
X-RAY DIFFRACTIONr_mcangle_other4.3435.87215742
X-RAY DIFFRACTIONr_scbond_it3.094.28711372
X-RAY DIFFRACTIONr_scbond_other2.9554.21411281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7516.23916752
X-RAY DIFFRACTIONr_long_range_B_refined10.65174.5198657
X-RAY DIFFRACTIONr_long_range_B_other10.64874.48798624
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)
11A154300.1
12B154300.1
21A153000.11
22C153000.11
31A147040.12
32D147040.12
41A158460.09
42E158460.09
51A155180.1
52F155180.1
61A154920.09
62G154920.09
71A149260.12
72H149260.12
81A157600.09
82I157600.09
91A154800.1
92J154800.1
101A152700.11
102K152700.11
111A125100.16
112L125100.16
121B152900.1
122C152900.1
131B145940.11
132D145940.11
141B154280.1
142E154280.1
151B156820.08
152F156820.08
161B155140.08
162G155140.08
171B148220.11
172H148220.11
181B154100.09
182I154100.09
191B154860.09
192J154860.09
201B153460.09
202K153460.09
211B123660.15
212L123660.15
221C145300.11
222D145300.11
231C153560.1
232E153560.1
241C153400.1
242F153400.1
251C155020.09
252G155020.09
261C147900.11
262H147900.11
271C153220.1
272I153220.1
281C153040.1
282J153040.1
291C153520.1
292K153520.1
301C123520.15
302L123520.15
311D147900.11
312E147900.11
321D146440.11
322F146440.11
331D146820.1
332G146820.1
341D150280.09
342H150280.09
351D147380.11
352I147380.11
361D146680.11
362J146680.11
371D145480.11
372K145480.11
381D126340.14
382L126340.14
391E155240.1
392F155240.1
401E155060.09
402G155060.09
411E150040.11
412H150040.11
421E158720.08
422I158720.08
431E155000.1
432J155000.1
441E153020.1
442K153020.1
451E125540.15
452L125540.15
461F155480.08
462G155480.08
471F149140.11
472H149140.11
481F154740.1
482I154740.1
491F156460.08
492J156460.08
501F153920.08
502K153920.08
511F123840.15
512L123840.15
521G149620.1
522H149620.1
531G155000.08
532I155000.08
541G154780.09
542J154780.09
551G155920.07
552K155920.07
561G124340.15
562L124340.15
571H149720.11
572I149720.11
581H149000.1
582J149000.1
591H148200.11
592K148200.11
601H127200.14
602L127200.14
611I154400.1
612J154400.1
621I153060.09
622K153060.09
631I125300.15
632L125300.15
641J152740.09
642K152740.09
651J124340.15
652L124340.15
661K124040.15
662L124040.15
LS refinement shellResolution: 2.607→2.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 344 -
Rwork0.327 6835 -
obs--85.38 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.094-1.4991-1.17473.5273-0.11233.498-0.3752-0.0271-0.33630.62870.11910.36350.3702-0.13690.25610.2845-0.09450.16510.2011-0.06570.544553.3993-13.769310.0757
29.25831.33320.24762.2370.25957.78340.2929-0.0481-0.83440.1304-0.04430.20450.9589-0.3816-0.24860.3629-0.16710.14230.0811-0.09840.383554.1574-20.72927.8374
30.64890.5724-0.45473.07570.63591.1136-0.10090.1825-0.1362-0.12140.14880.0138-0.1751-0.186-0.04790.23050.04330.04870.2632-0.04120.255656.93288.55776.0596
41.41562.5106-0.849710.12575.12258.53110.17520.38840.29880.15520.10880.7039-0.2449-1.0133-0.2840.09720.0457-0.01770.38740.07820.468442.91931.56850.7696
50.9239-0.66071.21045.4395-2.46186.65970.10870.03850.3599-0.10490.05470.17330.02210.5715-0.16340.29050.08410.12920.19760.05750.305649.913651.362322.3599
68.92791.65380.0832.25911.43141.5662-0.1441-0.5252-0.10920.28110.043-0.36440.1850.50590.1010.41010.080.04810.39170.23050.420353.750155.890933.2705
71.8954-0.2696-0.08094.5759-0.51761.5418-0.00690.131-0.01740.1150.02530.6406-0.1888-0.0713-0.01840.22540.16030.17480.16020.06910.331738.382647.220827.1812
80.7264-0.1228-0.00123.20460.32660.0776-0.05570.0037-0.1060.13650.0380.4281-0.0787-0.07480.01770.24410.13180.15820.2820.01680.244344.381325.588324.8544
92.2818-0.59920.69632.7541-3.05975.2083-0.13110.08890.07860.3326-0.0713-0.1941-1.75520.36480.20231.103-0.2246-0.02930.0654-0.06360.294779.926646.695822.0942
107.7604-4.64843.566111.07555.67189.0468-0.3944-0.7795-0.6303-0.72010.6360.3031-1.2814-0.1284-0.24160.8641-0.314-0.05750.25460.17880.383984.549252.04619.4463
110.62380.69030.14953.13790.24361.41860.05480.1297-0.22170.14150.0008-0.5975-0.30830.391-0.05560.1286-0.0195-0.02530.2706-0.03390.328179.810523.265222.7994
1217.26373.9243-5.85859.80051.57012.95730.0335-0.4748-0.08210.7899-0.1224-0.08490.18070.1780.08890.2471-0.0557-0.22760.29270.10540.290889.141631.634833.9701
137.9274-5.0884-0.50787.9118-3.41916.45270.1540.0411-0.1894-0.53810.01520.14480.6913-0.1648-0.16920.10250.0446-0.03850.18790.02280.226362.9929-14.694438.7575
140.73380.7009-1.57983.0895-2.64155.2946-0.02730.00910.04420.33320.15460.25370.0165-0.1018-0.12730.13920.1271-0.03610.3010.08610.331861.2172-11.233349.2399
151.1428-0.1138-0.22811.7834-0.03631.0717-0.1301-0.1027-0.21130.78220.24220.027-0.1358-0.0915-0.1120.38220.14180.07310.21840.03780.159157.915718.160441.4887
160.24660.3374-0.21893.8323-1.63530.91570.0994-0.1345-0.15260.0123-0.2277-0.6091-0.15390.15630.12820.25320.0766-0.04150.30950.04110.390767.4145.199139.6149
173.706-0.5674-0.87595.24930.00871.336-0.291-0.2341-0.68770.43630.00830.83050.3530.0420.28270.1646-0.06430.2140.1978-0.0610.549310.8475-13.351959.2249
184.4265-2.1423-2.18458.039-0.69889.18040.1582-0.1939-0.62130.19970.0190.31130.46950.2674-0.17720.1986-0.13520.05640.1556-0.09670.427211.4628-20.689456.785
190.75430.2648-0.16653.13340.95490.6794-0.08980.1717-0.1278-0.17190.06820.2681-0.1146-0.02770.02160.086-0.03310.02490.27-0.02130.324314.3988.788854.896
200.85242.49080.99087.44213.17855.53680.0114-0.05730.1375-0.0241-0.22330.6625-0.2327-0.4210.21190.10060.0279-0.05120.2671-0.0530.48680.01082.212450.0836
212.0382-0.11290.32773.8474-1.83455.553-0.11240.12780.44670.1881-0.11480.1325-0.32790.33020.22720.10640.0430.06020.17120.04340.31298.221851.686571.6351
224.5875-0.2148-0.46734.6103-0.3728.0397-0.0419-0.09880.63830.526-0.2146-0.1463-0.50620.28430.25650.22590.02760.05950.0550.03320.27737.695958.069680.0558
234.1496-2.3559-0.51551.79930.47370.1577-0.1529-0.1384-0.19870.20310.12140.30660.0143-0.01890.03150.14660.13280.21080.23260.0370.5251-5.017345.252978.7855
240.4816-0.43190.12242.9180.15030.1568-0.08930.0357-0.090.23460.0090.5565-0.0189-0.07740.08020.07890.03420.16240.2728-0.00510.43381.982927.632973.7651
250.5173-1.31030.26224.8507-1.06092.5652-0.16990.02410.31270.56910.0872-0.2032-0.9115-0.04750.08270.3771-0.0789-0.02530.2197-0.04360.481538.733745.55573.8754
265.34150.87651.97838.17732.29427.3923-0.02620.00110.6346-0.2267-0.0183-0.24-0.86390.05770.04450.185-0.09690.01670.10870.01670.18742.405950.700266.1022
270.48010.9892-0.06322.4795-0.03120.8410.03740.0191-0.17790.22710.0462-0.4197-0.07420.2598-0.08360.0673-0.0077-0.03350.3376-0.0520.393938.090822.775770.854
288.9935-0.9021-3.54837.82-0.3451.466-0.0326-0.7672-0.19050.8032-0.0717-0.0669-0.07860.32730.10430.2443-0.0653-0.17290.34890.00650.189247.940231.839382.0875
299.078-5.2219-1.0934.7988-0.90065.12140.16410.1744-0.3278-0.121-0.05850.29720.7576-0.0308-0.10560.1650.0309-0.04390.14670.02360.287721.4525-14.468586.8936
309.1334-1.641-6.1729.0629-2.87217.0391-0.01741.0347-0.7268-0.8452-0.27110.29411.3047-1.11060.28840.8839-0.3534-0.06230.33350.02990.221315.6221-22.415489.9262
310.14690.62920.0144.1803-0.05421.22850.0119-0.09480.07630.72120.06190.3444-0.14760.1474-0.07380.32680.1579-0.04620.28630.05260.299923.0166-2.854198.2894
320.43940.01570.15742.1726-0.07470.59130.1117-0.1932-0.13350.6680.0130.0053-0.0660.0598-0.12480.34570.05070.05330.28660.03840.254919.790412.586389.3365
330.9368-0.7272-0.78845.23260.45252.3646-0.07420.2628-0.5607-0.881-0.1849-0.11220.3667-0.07440.25910.2394-0.01280.10420.2075-0.0490.572614.7703-71.493538.514
3411.85488.8175-1.65436.5732-1.690114.8867-0.0480.35830.3724-0.01750.23690.2864-0.3820.8455-0.18890.38680.13630.13030.18830.00040.199415.1251-78.331133.2142
350.9834-0.6256-0.38052.4563-0.6270.9963-0.0688-0.0789-0.14670.02170.015-0.0549-0.0880.00430.05380.0798-0.0143-0.03860.24370.02430.29411.8009-51.077743.4021
360.8156-1.91811.75068.2251-1.19386.1678-0.05310.12610.083-0.10860.0084-0.4857-0.36110.67930.04470.0932-0.0924-0.04990.3440.06150.327925.9797-55.457847.4903
371.7020.58740.18366.18641.86611.005-0.0514-0.09170.481-0.3018-0.27070.4237-0.0757-0.26530.3220.3068-0.0001-0.03670.174-0.0310.314517.945-5.418123.0788
3814.0329-0.6059-1.222313.7016-3.21725.96740.25310.3894-0.07880.0388-0.6650.8654-0.117-0.45140.41180.3455-0.0042-0.05150.1792-0.13470.305212.15130.939922.6393
390.40890.7159-0.20562.58090.06860.89830.04190.0874-0.0681-0.3503-0.087-0.3866-0.13370.17990.04510.17510.04050.08140.28830.06680.293325.0527-26.424821.0956
405.2524-1.0425-2.51893.61921.96862.73370.0278-0.9451-0.29480.3146-0.0436-0.248-0.04290.24040.01580.17420.0012-0.01350.2780.10770.226528.2419-15.522533.0892
413.3637-1.6410.37285.45791.15050.7034-0.09110.07140.3783-0.04-0.01880.1243-0.3089-0.30280.10990.27290.30960.01760.380.1110.3066-17.3947-13.261229.6352
429.6256-0.79060.42493.85010.19280.0590.2113-0.4642-0.4532-0.1164-0.14240.610.0337-0.097-0.06890.1358-0.0388-0.08980.38550.10550.4467-28.2389-30.628931.1262
430.6418-0.9920.11532.6526-0.92931.27250.12260.2084-0.1318-0.15310.02110.372-0.1143-0.4347-0.14370.05930.0689-0.08250.44510.00310.309-8.3571-38.539726.3707
446.36180.67-1.08589.9644-3.10741.1986-0.26640.6195-0.2286-0.60680.0928-0.0170.059-0.21430.17350.29380.0793-0.21350.448-0.02280.234-22.2574-26.611216.6402
457.98693.57713.84677.86593.54852.41370.40670.0027-0.04820.1428-0.2761-0.34610.3231-0.1377-0.13060.7504-0.1345-0.09470.4338-0.03030.23432.3934-70.986811.277
460.8341.4422-1.06714.7944-0.30575.13410.0357-0.01390.0084-0.1943-0.069-0.1107-0.1796-0.16250.03330.228-0.1608-0.02020.3629-0.12130.11761.466-69.9253-1.3317
470.71620.3769-0.51591.2744-0.44592.13710.09420.4542-0.1526-0.3113-0.10090.00480.0457-0.18320.00670.23560.1223-0.07360.4677-0.04930.16547.0111-40.20999.7434
484.8043-0.04034.77310.11420.63369.36760.1961-0.1155-0.5357-0.05430.05690.01550.0779-0.3815-0.2530.3592-0.2053-0.10410.4908-0.15650.2076-5.3975-60.49016.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2A43 - 69
3X-RAY DIFFRACTION3A70 - 249
4X-RAY DIFFRACTION4A250 - 267
5X-RAY DIFFRACTION5B0 - 34
6X-RAY DIFFRACTION6B35 - 53
7X-RAY DIFFRACTION7B54 - 130
8X-RAY DIFFRACTION8B131 - 265
9X-RAY DIFFRACTION9C1 - 46
10X-RAY DIFFRACTION10C47 - 68
11X-RAY DIFFRACTION11C69 - 250
12X-RAY DIFFRACTION12C251 - 266
13X-RAY DIFFRACTION13D1 - 36
14X-RAY DIFFRACTION14D37 - 131
15X-RAY DIFFRACTION15D132 - 213
16X-RAY DIFFRACTION16D214 - 267
17X-RAY DIFFRACTION17E1 - 42
18X-RAY DIFFRACTION18E43 - 69
19X-RAY DIFFRACTION19E70 - 250
20X-RAY DIFFRACTION20E251 - 267
21X-RAY DIFFRACTION21F0 - 34
22X-RAY DIFFRACTION22F35 - 69
23X-RAY DIFFRACTION23F70 - 111
24X-RAY DIFFRACTION24F112 - 265
25X-RAY DIFFRACTION25G1 - 34
26X-RAY DIFFRACTION26G35 - 71
27X-RAY DIFFRACTION27G72 - 249
28X-RAY DIFFRACTION28G250 - 266
29X-RAY DIFFRACTION29H1 - 36
30X-RAY DIFFRACTION30H37 - 68
31X-RAY DIFFRACTION31H69 - 142
32X-RAY DIFFRACTION32H143 - 268
33X-RAY DIFFRACTION33I1 - 43
34X-RAY DIFFRACTION34I44 - 56
35X-RAY DIFFRACTION35I57 - 250
36X-RAY DIFFRACTION36I251 - 267
37X-RAY DIFFRACTION37J0 - 43
38X-RAY DIFFRACTION38J44 - 57
39X-RAY DIFFRACTION39J58 - 239
40X-RAY DIFFRACTION40J240 - 266
41X-RAY DIFFRACTION41K1 - 103
42X-RAY DIFFRACTION42K104 - 116
43X-RAY DIFFRACTION43K117 - 250
44X-RAY DIFFRACTION44K251 - 266
45X-RAY DIFFRACTION45L1 - 24
46X-RAY DIFFRACTION46L27 - 125
47X-RAY DIFFRACTION47L126 - 235
48X-RAY DIFFRACTION48L236 - 268

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