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- PDB-4esv: A New Twist on the Translocation Mechanism of Helicases from the ... -

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Basic information

Entry
Database: PDB / ID: 4esv
TitleA New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates
Components
  • 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • Replicative helicase
KeywordsHYDROLASE/DNA / RecA Fold / Helicase / HYDROLASE-DNA complex
Function / homology
Function and homology information


primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / isomerase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / ATP hydrolysis activity / DNA binding ...primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / isomerase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. ...DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.2 Å
AuthorsItsathitphaisarn, O. / Wing, R.A. / Eliason, W.K. / Wang, J. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.
Authors: Itsathitphaisarn, O. / Wing, R.A. / Eliason, W.K. / Wang, J. / Steitz, T.A.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Jun 6, 2018Group: Data collection / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / software / Item: _software.classification
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
W: 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
A: Replicative helicase
B: Replicative helicase
C: Replicative helicase
D: Replicative helicase
E: Replicative helicase
F: Replicative helicase
G: Replicative helicase
H: Replicative helicase
I: Replicative helicase
J: Replicative helicase
K: Replicative helicase
L: Replicative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)623,32052
Polymers616,51714
Non-polymers6,80438
Water905
1
V: 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
A: Replicative helicase
B: Replicative helicase
C: Replicative helicase
D: Replicative helicase
E: Replicative helicase
F: Replicative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,97330
Polymers308,4107
Non-polymers3,56223
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43410 Å2
ΔGint-327 kcal/mol
Surface area104070 Å2
MethodPISA
2
W: 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
G: Replicative helicase
H: Replicative helicase
I: Replicative helicase
J: Replicative helicase
K: Replicative helicase
L: Replicative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,34822
Polymers308,1067
Non-polymers3,24215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.124, 180.321, 279.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13G
23H
33I
43J
53L
14G
24H
34I
44J
54K
64L
15B
25C
35D
45E
55F
16G
26H
36I
46K
56J
17A
27B
37C
47D
57E
67F
18G
28H
38I
48J
58K
68L
19A
29B
39C
49D
59E
69F
110G
210H
310I
410J
510L
111A
211C
311D
411E
511F
112A
212C
312D
412E
512F

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA15 - 9415 - 94
211BB15 - 9415 - 94
311CC15 - 9415 - 94
411DD15 - 9415 - 94
511EE15 - 9415 - 94
611FF15 - 9415 - 94
112AA183 - 244183 - 244
212BB183 - 244183 - 244
312CC183 - 244183 - 244
412DD183 - 244183 - 244
512EE183 - 244183 - 244
612FF183 - 244183 - 244
122AA246 - 263246 - 263
222BB246 - 263246 - 263
322CC246 - 263246 - 263
422DD246 - 263246 - 263
522EE246 - 263246 - 263
622FF246 - 263246 - 263
132AA265 - 272265 - 272
232BB265 - 272265 - 272
332CC265 - 272265 - 272
432DD265 - 272265 - 272
532EE265 - 272265 - 272
632FF265 - 272265 - 272
142AA274 - 277274 - 277
242BB274 - 277274 - 277
342CC274 - 277274 - 277
442DD274 - 277274 - 277
542EE274 - 277274 - 277
642FF274 - 277274 - 277
152AA279 - 319279 - 319
252BB279 - 319279 - 319
352CC279 - 319279 - 319
452DD279 - 319279 - 319
552EE279 - 319279 - 319
652FF279 - 319279 - 319
162AA322 - 364322 - 364
262BB322 - 364322 - 364
362CC322 - 364322 - 364
462DD322 - 364322 - 364
562EE322 - 364322 - 364
662FF322 - 364322 - 364
172AA366 - 387366 - 387
272BB366 - 387366 - 387
372CC366 - 387366 - 387
472DD366 - 387366 - 387
572EE366 - 387366 - 387
672FF366 - 387366 - 387
182AA389 - 397389 - 397
282BB389 - 397389 - 397
382CC389 - 397389 - 397
482DD389 - 397389 - 397
582EE389 - 397389 - 397
682FF389 - 397389 - 397
113GG15 - 7715 - 77
213HH15 - 7715 - 77
313II15 - 7715 - 77
413JJ15 - 7715 - 77
513LL15 - 7715 - 77
123GG79 - 9479 - 94
223HH79 - 9479 - 94
323II79 - 9479 - 94
423JJ79 - 9479 - 94
523LL79 - 9479 - 94
114GG183 - 202183 - 202
214HH183 - 202183 - 202
314II183 - 202183 - 202
414JJ183 - 202183 - 202
514KK183 - 202183 - 202
614LL183 - 202183 - 202
124GG204 - 277204 - 277
224HH204 - 277204 - 277
324II204 - 277204 - 277
424JJ204 - 277204 - 277
524KK204 - 277204 - 277
624LL204 - 277204 - 277
134GG279 - 319279 - 319
234HH279 - 319279 - 319
334II279 - 319279 - 319
434JJ279 - 319279 - 319
534KK279 - 319279 - 319
634LL279 - 319279 - 319
144GG322 - 387322 - 387
244HH322 - 387322 - 387
344II322 - 387322 - 387
444JJ322 - 387322 - 387
544KK322 - 387322 - 387
644LL322 - 387322 - 387
154GG389 - 401389 - 401
254HH389 - 401389 - 401
354II389 - 401389 - 401
454JJ389 - 401389 - 401
554KK389 - 401389 - 401
654LL389 - 401389 - 401
164GG403 - 441403 - 441
264HH403 - 441403 - 441
364II403 - 441403 - 441
464JJ403 - 441403 - 441
564KK403 - 441403 - 441
664LL403 - 441403 - 441
115BB161 - 167161 - 167
215CC161 - 167161 - 167
315DD161 - 167161 - 167
415EE161 - 167161 - 167
515FF161 - 167161 - 167
125BB171 - 172171 - 172
225CC171 - 172171 - 172
325DD171 - 172171 - 172
425EE171 - 172171 - 172
525FF171 - 172171 - 172
135BB174 - 176174 - 176
235CC174 - 176174 - 176
335DD174 - 176174 - 176
435EE174 - 176174 - 176
535FF174 - 176174 - 176
116GG161 - 176161 - 176
216HH161 - 176161 - 176
316II161 - 176161 - 176
416KK161 - 176161 - 176
516JJ161 - 176161 - 176
117AA141 - 149141 - 149
217BB141 - 149141 - 149
317CC141 - 149141 - 149
417DD141 - 149141 - 149
517EE141 - 149141 - 149
617FF141 - 149141 - 149
118GG141 - 149141 - 149
218HH141 - 149141 - 149
318II141 - 149141 - 149
418JJ141 - 149141 - 149
518KK141 - 149141 - 149
618LL141 - 149141 - 149
119AA101 - 103101 - 103
219BB101 - 103101 - 103
319CC101 - 103101 - 103
419DD101 - 103101 - 103
519EE101 - 103101 - 103
619FF101 - 103101 - 103
129AA105 - 134105 - 134
229BB105 - 134105 - 134
329CC105 - 134105 - 134
429DD105 - 134105 - 134
529EE105 - 134105 - 134
629FF105 - 134105 - 134
139AA136 - 139136 - 139
239BB136 - 139136 - 139
339CC136 - 139136 - 139
439DD136 - 139136 - 139
539EE136 - 139136 - 139
639FF136 - 139136 - 139
1110GG101 - 103101 - 103
2110HH101 - 103101 - 103
3110II101 - 103101 - 103
4110JJ101 - 103101 - 103
5110LL101 - 103101 - 103
1210GG105 - 134105 - 134
2210HH105 - 134105 - 134
3210II105 - 134105 - 134
4210JJ105 - 134105 - 134
5210LL105 - 134105 - 134
1310GG136 - 139136 - 139
2310HH136 - 139136 - 139
3310II136 - 139136 - 139
4310JJ136 - 139136 - 139
5310LL136 - 139136 - 139
1111AA410 - 441410 - 441
2111CC410 - 441410 - 441
3111DD410 - 441410 - 441
4111EE410 - 441410 - 441
5111FF410 - 441410 - 441
1112AA398 - 409398 - 409
2112CC398 - 409398 - 409
3112DD398 - 409398 - 409
4112EE398 - 409398 - 409
5112FF398 - 409398 - 409

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

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Components

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DNA chain , 2 types, 2 molecules VW

#1: DNA chain 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 4213.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 3909.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#3: Protein
Replicative helicase / DnaB


Mass: 50699.445 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: dnaB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X4C9, DNA helicase

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Non-polymers , 5 types, 43 molecules

#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: AlF4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4-7% PEG3350, 0.2 M calcium chloride, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.11
SYNCHROTRONNSLS X2521.2545,1.2300,1.2549
SYNCHROTRONNSLS X29A31.11
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCD
DECTRIS PILATUS 6M2PIXELApr 4, 2011
ADSC QUANTUM 3153CCDJun 17, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
3Rosenbaum-Rock double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.111
21.25451
31.231
41.25491
ReflectionResolution: 3.2→50 Å / Num. all: 124032 / Num. obs: 124032 / % possible obs: 88.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.115 / Χ2: 1.136 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.2-3.422.897461.1151,2,387.6
3.42-3.552.997551.1341,2,387.40.738
3.55-3.72397581.1421,2,387.50.547
3.72-3.91397941.1631,2,387.60.378
3.91-4.163.198081.1891,2,387.70.251
4.16-4.483.198761.1911,2,388.10.157
4.48-4.933.1100301.1941,2,389.10.116
4.93-5.643.1100981.1711,2,389.40.122
5.64-7.13102061.0691,2,389.50.094
7.1-503.1104980.9971,2,389.30.044

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHELXmodel building
REFMAC5.5.0109refinement
PDB_EXTRACT3.006data extraction
ADSCdata collection
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.2→47.92 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 0 / SU B: 64.177 / SU ML: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.613 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 5442 5 %RANDOM
Rwork0.242 ---
obs0.245 108863 87.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 331.2 Å2 / Biso mean: 140.749 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0 Å2
2--0.03 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39351 540 392 5 40288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02240847
X-RAY DIFFRACTIONr_angle_refined_deg1.5062.00255365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34455038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96724.6721873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.808157319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.87415342
X-RAY DIFFRACTIONCHIRAL-CEN RESTRAINTS (A**3)0.1130.26455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02130127
X-RAY DIFFRACTIONr_mcbond_it3.266625229
X-RAY DIFFRACTIONr_mcangle_it5.949840660
X-RAY DIFFRACTIONr_scbond_it5.329815618
X-RAY DIFFRACTIONr_scangle_it9.1941214705
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A316TIGHT POSITIONAL0.030.05
1B316TIGHT POSITIONAL0.030.05
1C316TIGHT POSITIONAL0.030.05
1D316TIGHT POSITIONAL0.030.05
1E316TIGHT POSITIONAL0.030.05
1F316TIGHT POSITIONAL0.030.05
1A279MEDIUM POSITIONAL0.040.5
1B279MEDIUM POSITIONAL0.040.5
1C279MEDIUM POSITIONAL0.040.5
1D279MEDIUM POSITIONAL0.040.5
1E279MEDIUM POSITIONAL0.040.5
1F279MEDIUM POSITIONAL0.030.5
1A316TIGHT THERMAL3.582.5
1B316TIGHT THERMAL3.512.5
1C316TIGHT THERMAL2.222.5
1D316TIGHT THERMAL2.862.5
1E316TIGHT THERMAL2.242.5
1F316TIGHT THERMAL3.52.5
1A279MEDIUM THERMAL3.810
1B279MEDIUM THERMAL3.4210
1C279MEDIUM THERMAL2.2310
1D279MEDIUM THERMAL2.8410
1E279MEDIUM THERMAL2.1610
1F279MEDIUM THERMAL3.2810
2A791TIGHT POSITIONAL0.050.05
2B791TIGHT POSITIONAL0.050.05
2C791TIGHT POSITIONAL0.060.05
2D791TIGHT POSITIONAL0.040.05
2E791TIGHT POSITIONAL0.040.05
2F791TIGHT POSITIONAL0.040.05
2A701MEDIUM POSITIONAL0.060.5
2B701MEDIUM POSITIONAL0.060.5
2C701MEDIUM POSITIONAL0.060.5
2D701MEDIUM POSITIONAL0.050.5
2E701MEDIUM POSITIONAL0.050.5
2F701MEDIUM POSITIONAL0.050.5
2A791TIGHT THERMAL3.012.5
2B791TIGHT THERMAL5.282.5
2C791TIGHT THERMAL4.182.5
2D791TIGHT THERMAL1.982.5
2E791TIGHT THERMAL2.342.5
2F791TIGHT THERMAL1.972.5
2A701MEDIUM THERMAL2.9710
2B701MEDIUM THERMAL5.4710
2C701MEDIUM THERMAL3.8910
2D701MEDIUM THERMAL2.0610
2E701MEDIUM THERMAL2.2210
2F701MEDIUM THERMAL1.9510
3G312TIGHT POSITIONAL0.030.05
3H312TIGHT POSITIONAL0.030.05
3I312TIGHT POSITIONAL0.040.05
3J312TIGHT POSITIONAL0.030.05
3L312TIGHT POSITIONAL0.030.05
3G274MEDIUM POSITIONAL0.030.5
3H274MEDIUM POSITIONAL0.040.5
3I274MEDIUM POSITIONAL0.030.5
3J274MEDIUM POSITIONAL0.040.5
3L274MEDIUM POSITIONAL0.030.5
3G312TIGHT THERMAL2.322.5
3H312TIGHT THERMAL3.112.5
3I312TIGHT THERMAL3.252.5
3J312TIGHT THERMAL2.92.5
3L312TIGHT THERMAL6.492.5
3G274MEDIUM THERMAL2.310
3H274MEDIUM THERMAL2.9810
3I274MEDIUM THERMAL3.2510
3J274MEDIUM THERMAL2.8310
3L274MEDIUM THERMAL6.4910
4G988TIGHT POSITIONAL0.020.05
4H988TIGHT POSITIONAL0.030.05
4I988TIGHT POSITIONAL0.030.05
4J988TIGHT POSITIONAL0.020.05
4K988TIGHT POSITIONAL0.020.05
4L988TIGHT POSITIONAL0.020.05
4G925MEDIUM POSITIONAL0.030.5
4H925MEDIUM POSITIONAL0.030.5
4I925MEDIUM POSITIONAL0.030.5
4J925MEDIUM POSITIONAL0.020.5
4K925MEDIUM POSITIONAL0.030.5
4L925MEDIUM POSITIONAL0.030.5
4G988TIGHT THERMAL3.612.5
4H988TIGHT THERMAL3.72.5
4I988TIGHT THERMAL3.352.5
4J988TIGHT THERMAL4.052.5
4K988TIGHT THERMAL3.182.5
4L988TIGHT THERMAL1.522.5
4G925MEDIUM THERMAL3.510
4H925MEDIUM THERMAL3.7710
4I925MEDIUM THERMAL3.3810
4J925MEDIUM THERMAL3.8610
4K925MEDIUM THERMAL2.9410
4L925MEDIUM THERMAL1.6410
5B40TIGHT POSITIONAL0.030.05
5C40TIGHT POSITIONAL0.030.05
5D40TIGHT POSITIONAL0.030.05
5E40TIGHT POSITIONAL0.030.05
5F40TIGHT POSITIONAL0.040.05
5B41MEDIUM POSITIONAL0.040.5
5C41MEDIUM POSITIONAL0.030.5
5D41MEDIUM POSITIONAL0.030.5
5E41MEDIUM POSITIONAL0.030.5
5F41MEDIUM POSITIONAL0.040.5
5B40TIGHT THERMAL4.312.5
5C40TIGHT THERMAL2.162.5
5D40TIGHT THERMAL1.972.5
5E40TIGHT THERMAL4.942.5
5F40TIGHT THERMAL1.422.5
5B41MEDIUM THERMAL3.4810
5C41MEDIUM THERMAL1.6210
5D41MEDIUM THERMAL1.9810
5E41MEDIUM THERMAL4.3110
5F41MEDIUM THERMAL1.7910
6G52TIGHT POSITIONAL0.040.05
6H52TIGHT POSITIONAL0.050.05
6I52TIGHT POSITIONAL0.020.05
6K52TIGHT POSITIONAL0.020.05
6J52TIGHT POSITIONAL0.020.05
6G53MEDIUM POSITIONAL0.050.5
6H53MEDIUM POSITIONAL0.020.5
6I53MEDIUM POSITIONAL0.020.5
6K53MEDIUM POSITIONAL0.020.5
6J53MEDIUM POSITIONAL0.020.5
6G52TIGHT THERMAL1.342.5
6H52TIGHT THERMAL5.322.5
6I52TIGHT THERMAL4.822.5
6K52TIGHT THERMAL1.482.5
6J52TIGHT THERMAL1.532.5
6G53MEDIUM THERMAL1.5110
6H53MEDIUM THERMAL4.6510
6I53MEDIUM THERMAL5.3510
6K53MEDIUM THERMAL1.510
6J53MEDIUM THERMAL1.3210
7A36TIGHT POSITIONAL0.030.05
7B36TIGHT POSITIONAL0.030.05
7C36TIGHT POSITIONAL0.030.05
7D36TIGHT POSITIONAL0.020.05
7E36TIGHT POSITIONAL0.020.05
7F36TIGHT POSITIONAL0.020.05
7A39MEDIUM POSITIONAL0.040.5
7B39MEDIUM POSITIONAL0.030.5
7C39MEDIUM POSITIONAL0.030.5
7D39MEDIUM POSITIONAL0.030.5
7E39MEDIUM POSITIONAL0.030.5
7F39MEDIUM POSITIONAL0.030.5
7A36TIGHT THERMAL4.562.5
7B36TIGHT THERMAL3.622.5
7C36TIGHT THERMAL1.022.5
7D36TIGHT THERMAL2.642.5
7E36TIGHT THERMAL4.142.5
7F36TIGHT THERMAL2.192.5
7A39MEDIUM THERMAL3.6710
7B39MEDIUM THERMAL2.6810
7C39MEDIUM THERMAL1.0110
7D39MEDIUM THERMAL2.1410
7E39MEDIUM THERMAL3.9810
7F39MEDIUM THERMAL1.810
8G36TIGHT POSITIONAL0.020.05
8H36TIGHT POSITIONAL0.030.05
8I36TIGHT POSITIONAL0.020.05
8J36TIGHT POSITIONAL0.030.05
8K36TIGHT POSITIONAL0.020.05
8L36TIGHT POSITIONAL0.020.05
8G39MEDIUM POSITIONAL0.030.5
8H39MEDIUM POSITIONAL0.030.5
8I39MEDIUM POSITIONAL0.030.5
8J39MEDIUM POSITIONAL0.030.5
8K39MEDIUM POSITIONAL0.030.5
8L39MEDIUM POSITIONAL0.030.5
8G36TIGHT THERMAL1.112.5
8H36TIGHT THERMAL1.252.5
8I36TIGHT THERMAL2.392.5
8J36TIGHT THERMAL2.412.5
8K36TIGHT THERMAL1.642.5
8L36TIGHT THERMAL2.212.5
8G39MEDIUM THERMAL1.0110
8H39MEDIUM THERMAL1.3310
8I39MEDIUM THERMAL2.210
8J39MEDIUM THERMAL2.410
8K39MEDIUM THERMAL1.5210
8L39MEDIUM THERMAL1.710
9A148TIGHT POSITIONAL0.040.05
9B148TIGHT POSITIONAL0.050.05
9C148TIGHT POSITIONAL0.040.05
9D148TIGHT POSITIONAL0.040.05
9E148TIGHT POSITIONAL0.030.05
9F148TIGHT POSITIONAL0.030.05
9A153MEDIUM POSITIONAL0.060.5
9B153MEDIUM POSITIONAL0.060.5
9C153MEDIUM POSITIONAL0.060.5
9D153MEDIUM POSITIONAL0.040.5
9E153MEDIUM POSITIONAL0.050.5
9F153MEDIUM POSITIONAL0.040.5
9A148TIGHT THERMAL5.152.5
9B148TIGHT THERMAL3.112.5
9C148TIGHT THERMAL2.822.5
9D148TIGHT THERMAL1.892.5
9E148TIGHT THERMAL4.972.5
9F148TIGHT THERMAL4.522.5
9A153MEDIUM THERMAL4.4610
9B153MEDIUM THERMAL2.9710
9C153MEDIUM THERMAL2.9910
9D153MEDIUM THERMAL1.9310
9E153MEDIUM THERMAL4.4110
9F153MEDIUM THERMAL4.2510
10G148TIGHT POSITIONAL0.030.05
10H148TIGHT POSITIONAL0.030.05
10I148TIGHT POSITIONAL0.040.05
10J148TIGHT POSITIONAL0.030.05
10L148TIGHT POSITIONAL0.030.05
10G153MEDIUM POSITIONAL0.040.5
10H153MEDIUM POSITIONAL0.040.5
10I153MEDIUM POSITIONAL0.050.5
10J153MEDIUM POSITIONAL0.040.5
10L153MEDIUM POSITIONAL0.030.5
10G148TIGHT THERMAL2.072.5
10H148TIGHT THERMAL1.462.5
10I148TIGHT THERMAL3.882.5
10J148TIGHT THERMAL3.442.5
10L148TIGHT THERMAL4.242.5
10G153MEDIUM THERMAL1.6610
10H153MEDIUM THERMAL1.510
10I153MEDIUM THERMAL3.8210
10J153MEDIUM THERMAL3.2510
10L153MEDIUM THERMAL4.8510
11A128TIGHT POSITIONAL0.060.05
11C128TIGHT POSITIONAL0.040.05
11D128TIGHT POSITIONAL0.040.05
11E128TIGHT POSITIONAL0.040.05
11F128TIGHT POSITIONAL0.040.05
11A129MEDIUM POSITIONAL0.070.5
11C129MEDIUM POSITIONAL0.060.5
11D129MEDIUM POSITIONAL0.040.5
11E129MEDIUM POSITIONAL0.040.5
11F129MEDIUM POSITIONAL0.050.5
11A128TIGHT THERMAL2.192.5
11C128TIGHT THERMAL3.542.5
11D128TIGHT THERMAL1.622.5
11E128TIGHT THERMAL2.542.5
11F128TIGHT THERMAL2.362.5
11A129MEDIUM THERMAL2.4510
11C129MEDIUM THERMAL3.7510
11D129MEDIUM THERMAL1.8210
11E129MEDIUM THERMAL2.5210
11F129MEDIUM THERMAL2.3710
12A48TIGHT POSITIONAL0.040.05
12C48TIGHT POSITIONAL0.040.05
12D48TIGHT POSITIONAL0.030.05
12E48TIGHT POSITIONAL0.030.05
12F48TIGHT POSITIONAL0.040.05
12A60MEDIUM POSITIONAL0.040.5
12C60MEDIUM POSITIONAL0.050.5
12D60MEDIUM POSITIONAL0.030.5
12E60MEDIUM POSITIONAL0.030.5
12F60MEDIUM POSITIONAL0.050.5
12A48TIGHT THERMAL1.32.5
12C48TIGHT THERMAL2.812.5
12D48TIGHT THERMAL1.292.5
12E48TIGHT THERMAL1.752.5
12F48TIGHT THERMAL1.542.5
12A60MEDIUM THERMAL1.2810
12C60MEDIUM THERMAL2.4210
12D60MEDIUM THERMAL1.1810
12E60MEDIUM THERMAL1.4410
12F60MEDIUM THERMAL1.5710
LS refinement shellResolution: 3.2→3.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 344 -
Rwork0.354 6962 -
all-7306 -
obs--80.82 %
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)
13.46560.7758-3.90490.2468-0.90784.8255-0.0305-0.1752-0.1992-0.17690.1525-0.04670.17760.184-0.1220.88590.02220.13070.9139-0.12140.6993122.40937.61752.014
20.28140.0172-0.31250.97260.26120.48760.04640.1752-0.02470.1073-0.0698-0.06190.0319-0.01860.02350.76450.05320.1620.826-0.11990.8917130.31761.5377.085
39.2722.5673-7.01441.0358-1.96495.3635-0.30330.33130.6031-0.29070.67810.30520.4369-0.1881-0.37480.6523-0.0047-0.04891.18670.18280.64986.30532.12278.844
43.5138-0.1277-0.99020.4001-0.13530.46740.12090.39750.28190.1535-0.0382-0.04990.01330.2202-0.08270.61840.12730.05661.07940.10910.8212130.80121.87990.345
50.7524-0.0832-0.75851.56480.41231.089-0.12230.03520.01720.0740.2083-0.1598-0.0042-0.4638-0.0860.63740.0694-0.07740.98250.13780.900656.94740.526100.462
60.908-0.2797-0.3391.1036-0.22520.45860.1115-0.0908-0.088-0.1149-0.03720.28020.02820.1978-0.07420.6986-0.0052-0.03790.8310.1230.9099103.37517.205107.998
71.34143.2083-0.19597.8504-0.58870.1126-0.30350.1526-0.5349-0.35270.4723-1.0218-0.1266-0.1189-0.16880.90560.21860.05650.4493-0.09641.34276.33281.38998.675
80.6448-0.4848-0.12081.90520.49810.1749-0.0667-0.1892-0.06360.23410.1140.2838-0.07240.0957-0.04730.7172-0.00270.13410.99250.00570.764390.13740.995126.332
92.3066-1.5598-1.25211.38551.20861.16240.3101-0.0676-0.0994-0.2317-0.0065-0.2042-0.4530.0077-0.30361.04830.22090.09860.4913-0.26381.015593.456113.41486.36
100.71490.7894-0.50621.2795-0.24150.70770.177-0.16090.14650.0261-0.02930.0114-0.2164-0.0463-0.14770.84760.01640.12930.8842-0.25620.7812101.36971.655124.949
111.3343-1.0403-1.30152.4913.24894.2717-0.0464-0.0389-0.0312-0.2919-0.0109-0.0054-0.4744-0.16170.05731.00470.28660.1840.6285-0.18820.8552110.81286.42454.645
121.06730.1195-0.91730.17810.16931.25260.1611-0.1060.1969-0.03870.0096-0.0391-0.21390.0546-0.17070.8615-0.05270.15270.6293-0.21560.9993122.76281.09101.904
130.4231.11661.3232.97293.49394.3146-0.0619-0.04860.1545-0.0492-0.16790.45080.02050.08430.22981.1319-0.0860.06820.5846-0.26130.7926106.75358.61519.746
141.4545-0.6982-0.03290.39690.13561.74660.14230.43790.37760.1547-0.204-0.1330.09420.03150.06170.93180.20330.1030.89110.15280.7568133.28560.282-6.882
150.04660.14790.07922.72442.08421.69030.0627-0.0023-0.1727-0.0257-0.15370.0382-0.2929-0.06710.0910.8944-0.01870.06990.7058-0.1840.950694.05922.523-4.44
160.7469-0.62640.55061.3901-0.22860.5912-0.15910.24140.33970.1198-0.0964-0.12860.06430.45320.25550.62470.31580.08660.73250.21920.392594.64667.683-20.427
173.15781.96510.63221.54360.59040.27260.28990.1808-0.1728-0.0617-0.2424-0.034-0.0066-0.1985-0.04750.66850.05230.05270.676-0.15581.169895.452-7.399-26.575
180.4583-0.29080.40890.2317-0.32860.53280.26370.10660.0347-0.2016-0.09910.11130.53780.2869-0.16471.2380.79540.10810.6680.16560.416785.13940.905-36.664
193.67381.2149-0.59360.4128-0.20810.13510.21660.08820.2690.1228-0.03370.1663-0.00410.1289-0.18290.47090.11490.24170.9888-0.04021.059139.313.804-26.781
200.426-0.513-0.49310.68550.66250.64060.18590.2625-0.0697-0.0225-0.14530.0112-0.0018-0.0763-0.04061.64331.397-0.19571.1986-0.18190.1191105.70123.249-54.807
211.5409-1.8327-0.94432.36811.59721.7966-0.0357-0.3050.05610.06320.3364-0.13640.09240.0634-0.30070.77360.17380.2210.7586-0.23681.0412173.27215.726-15.639
220.83360.1160.61050.01820.08790.53080.21880.6175-0.16680.05620.0472-0.02130.03670.3374-0.26610.98041.02350.15541.6465-0.06140.1849137.81328.841-53.078
231.903-1.8939-4.48481.9844.744711.4015-0.00930.16530.1740.1626-0.17920.02010.6503-0.31420.18841.33830.68750.56851.0346-0.0670.5514149.15337.02715.882
241.0193-0.1462-0.49730.07280.09270.75270.28910.55520.08790.0481-0.0968-0.1097-0.23550.0255-0.19230.65950.37980.22811.47220.28220.5126150.25649.376-30.437
250.0594-0.1966-0.26730.72690.98841.43740.0558-0.004-0.0735-0.05710.04680.0932-0.2281-0.0186-0.10250.6560.1118-0.00891.0379-0.04330.9397111.00350.726103.52
260.57880.3628-1.00470.2325-0.63511.83320.1985-0.14290.07170.0913-0.06360.0744-0.14610.4565-0.13491.11760.2728-0.04771.1587-0.03180.926117.95845.706-33.494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 149
2X-RAY DIFFRACTION2A183 - 441
3X-RAY DIFFRACTION2A502
4X-RAY DIFFRACTION2A161 - 170
5X-RAY DIFFRACTION3B15 - 149
6X-RAY DIFFRACTION4B183 - 441
7X-RAY DIFFRACTION4B161 - 178
8X-RAY DIFFRACTION5C15 - 149
9X-RAY DIFFRACTION6C183 - 441
10X-RAY DIFFRACTION6C501
11X-RAY DIFFRACTION6C161 - 179
12X-RAY DIFFRACTION7D15 - 149
13X-RAY DIFFRACTION8D183 - 441
14X-RAY DIFFRACTION8D501
15X-RAY DIFFRACTION8D161 - 179
16X-RAY DIFFRACTION9E15 - 149
17X-RAY DIFFRACTION10E183 - 441
18X-RAY DIFFRACTION10E501
19X-RAY DIFFRACTION10E161 - 178
20X-RAY DIFFRACTION11F15 - 149
21X-RAY DIFFRACTION12F183 - 441
22X-RAY DIFFRACTION12F501
23X-RAY DIFFRACTION12F161 - 176
24X-RAY DIFFRACTION13G15 - 149
25X-RAY DIFFRACTION14G183 - 441
26X-RAY DIFFRACTION14G501
27X-RAY DIFFRACTION15H15 - 149
28X-RAY DIFFRACTION16H183 - 441
29X-RAY DIFFRACTION16H161 - 179
30X-RAY DIFFRACTION17I15 - 149
31X-RAY DIFFRACTION18I183 - 441
32X-RAY DIFFRACTION18I501
33X-RAY DIFFRACTION18I161 - 176
34X-RAY DIFFRACTION19J15 - 149
35X-RAY DIFFRACTION20J183 - 441
36X-RAY DIFFRACTION20J501
37X-RAY DIFFRACTION20J161 - 176
38X-RAY DIFFRACTION21K15 - 149
39X-RAY DIFFRACTION22K183 - 441
40X-RAY DIFFRACTION22K501
41X-RAY DIFFRACTION22K161 - 176
42X-RAY DIFFRACTION23L15 - 149
43X-RAY DIFFRACTION24L183 - 441
44X-RAY DIFFRACTION24L501
45X-RAY DIFFRACTION24L161 - 176
46X-RAY DIFFRACTION25V1 - 13
47X-RAY DIFFRACTION26W1 - 13

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