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- PDB-7s81: Structure of human PARP1 domains (Zn1, Zn3, WGR, HD) bound to a D... -

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Basic information

Entry
Database: PDB / ID: 7s81
TitleStructure of human PARP1 domains (Zn1, Zn3, WGR, HD) bound to a DNA double strand break.
Components
  • (Poly [ADP-ribose] polymerase ...) x 3
  • DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
KeywordsDNA BINDING PROTEIN / PARP / ADP-ribose transferase / DNA break detection / zinc finger
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / single-strand break-containing DNA binding / mitochondrial DNA repair / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / ATP generation from poly-ADP-D-ribose / replication fork reversal / positive regulation of necroptotic process / establishment of protein localization to chromatin / positive regulation of intracellular estrogen receptor signaling pathway / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / single strand break repair / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / cellular response to zinc ion / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / decidualization / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / protein autoprocessing / macrophage differentiation / R-SMAD binding / negative regulation of adipose tissue development / nuclear replication fork / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / transforming growth factor beta receptor signaling pathway / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / response to gamma radiation / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / protein modification process / site of DNA damage / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / positive regulation of protein localization to nucleus / protein-DNA complex / fibrillar center / transcription by RNA polymerase II / DNA Damage Recognition in GG-NER / NAD binding / cellular response to amyloid-beta / histone deacetylase binding / enzyme activator activity / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / cellular response to UV / double-strand break repair / cellular response to insulin stimulus / nuclear envelope / regulation of protein localization / site of double-strand break / transcription regulator complex / cellular response to oxidative stress / damaged DNA binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / apoptotic process / chromatin binding / DNA damage response / nucleolus
Similarity search - Function
Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsRouleau-Turcotte, E. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT173370 Canada
CitationJournal: Mol.Cell / Year: 2022
Title: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery.
Authors: Rouleau-Turcotte, E. / Krastev, D.B. / Pettitt, S.J. / Lord, C.J. / Pascal, J.M.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 31, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
C: Poly [ADP-ribose] polymerase 1
K: Poly [ADP-ribose] polymerase 1
E: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
N: Poly [ADP-ribose] polymerase 1
I: Poly [ADP-ribose] polymerase 1
A: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
P: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
O: Poly [ADP-ribose] polymerase 1
J: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,41224
Polymers259,88916
Non-polymers5238
Water1267
1
M: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
K: Poly [ADP-ribose] polymerase 1
N: Poly [ADP-ribose] polymerase 1
I: Poly [ADP-ribose] polymerase 1
P: Poly [ADP-ribose] polymerase 1
O: Poly [ADP-ribose] polymerase 1
J: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,20612
Polymers129,9448
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Poly [ADP-ribose] polymerase 1
E: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
A: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,20612
Polymers129,9448
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.759, 128.552, 227.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))
21(chain F and (resid 7 through 9 or resid 11 through 200))
31(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))
41(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))
12(chain B and (resid 229 through 232 or resid 234 through 400))
22(chain G and (resid 229 through 232 or resid 234 through 400))
32(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))
42(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))
13(chain C and (resid 532 through 577 or resid 581...
23(chain H and (resid 532 through 577 or resid 581...
33(chain K and (resid 532 through 577 or resid 581...
43(chain P and (resid 532 through 577 or resid 581...
14chain D
24chain E
34chain L
44chain M

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSTYRTYR(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AI7 - 927 - 29
121VALVALGLUGLU(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AI11 - 9031 - 110
131ZNZNZNZN(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AS200
211LYSLYSTYRTYR(chain F and (resid 7 through 9 or resid 11 through 200))FO7 - 927 - 29
221VALVALZNZN(chain F and (resid 7 through 9 or resid 11 through 200))FO - W11 - 20031
311LYSLYSTYRTYR(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IH7 - 927 - 29
321VALVALGLUGLU(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IH11 - 9031 - 110
331ZNZNZNZN(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IR200
411LYSLYSTYRTYR(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NG7 - 927 - 29
421VALVALGLUGLU(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NG11 - 9031 - 110
431ZNZNZNZN(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NQ200
112ASPASPSERSER(chain B and (resid 229 through 232 or resid 234 through 400))BP229 - 23215 - 18
122LEULEUZNZN(chain B and (resid 229 through 232 or resid 234 through 400))BP - X234 - 40020
212ASPASPSERSER(chain G and (resid 229 through 232 or resid 234 through 400))GJ229 - 23215 - 18
222LEULEUZNZN(chain G and (resid 229 through 232 or resid 234 through 400))GJ - T234 - 40020
312ASPASPSERSER(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JN229 - 23215 - 18
322LEULEUPROPRO(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JN234 - 35820 - 144
332ZNZNZNZN(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JV400
412ASPASPSERSER(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OM229 - 23215 - 18
422LEULEUPROPRO(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OM234 - 35820 - 144
432ZNZNZNZN(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OU400
113ALAALAASPASP(chain C and (resid 532 through 577 or resid 581...CC532 - 57726 - 71
123ASNASNILEILE(chain C and (resid 532 through 577 or resid 581...CC581 - 64375 - 137
133LYSLYSSERSER(chain C and (resid 532 through 577 or resid 581...CC695 - 702175 - 182
143ARGARGTYRTYR(chain C and (resid 532 through 577 or resid 581...CC704 - 775184 - 255
213ALAALAASPASP(chain H and (resid 532 through 577 or resid 581...HL532 - 57726 - 71
223ASNASNILEILE(chain H and (resid 532 through 577 or resid 581...HL581 - 64375 - 137
233LYSLYSSERSER(chain H and (resid 532 through 577 or resid 581...HL695 - 702175 - 182
243ARGARGTYRTYR(chain H and (resid 532 through 577 or resid 581...HL704 - 775184 - 255
313ALAALAASPASP(chain K and (resid 532 through 577 or resid 581...KD532 - 57726 - 71
323ASNASNILEILE(chain K and (resid 532 through 577 or resid 581...KD581 - 64375 - 137
333LYSLYSSERSER(chain K and (resid 532 through 577 or resid 581...KD695 - 702175 - 182
343ARGARGTYRTYR(chain K and (resid 532 through 577 or resid 581...KD704 - 775184 - 255
413ALAALAASPASP(chain P and (resid 532 through 577 or resid 581...PK532 - 57726 - 71
423ASNASNILEILE(chain P and (resid 532 through 577 or resid 581...PK581 - 64375 - 137
433LYSLYSSERSER(chain P and (resid 532 through 577 or resid 581...PK695 - 702175 - 182
443ARGARGTYRTYR(chain P and (resid 532 through 577 or resid 581...PK704 - 775184 - 255
114DADADTDTchain DDF1 - 121 - 12
214DADADTDTchain EEE15 - 261 - 12
314DADADTDTchain LLB15 - 261 - 12
414DADADTDTchain MMA1 - 121 - 12

NCS ensembles :
ID
1
2
3
4

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Components

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DNA chain , 1 types, 4 molecules MLED

#1: DNA chain
DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')


Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Poly [ADP-ribose] polymerase ... , 3 types, 12 molecules CKPHNIAFGOJB

#2: Protein
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 29813.668 Da / Num. of mol.: 4 / Fragment: WGR domain and helical domain (HD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Protein
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 13101.821 Da / Num. of mol.: 4 / Fragment: first zinc finger (Zn1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#4: Protein
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


Mass: 18393.297 Da / Num. of mol.: 4 / Fragment: third zinc finger (Zn3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli)
References: UniProt: P09874, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 2 types, 15 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tert-butanol, Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→49.35 Å / Num. obs: 36391 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 13.8 / Num. measured all: 414757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.6-3.7611.91.2935200443860.8070.3911.3522100
12.47-49.3510.10.04399089830.9990.0140.04556.698.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQY

4dqy


Resolution: 3.6→49.35 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 41.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3122 1824 5.1 %
Rwork0.2516 33955 -
obs0.2547 35779 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 457.51 Å2 / Biso mean: 219.3711 Å2 / Biso min: 82.64 Å2
Refinement stepCycle: final / Resolution: 3.6→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13492 972 8 7 14479
Biso mean--203.08 83.97 -
Num. residues----1754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A681X-RAY DIFFRACTIONPOSITIONAL0.01
12F681X-RAY DIFFRACTIONPOSITIONAL0.01
13I681X-RAY DIFFRACTIONPOSITIONAL0.006
14N681X-RAY DIFFRACTIONPOSITIONAL0.007
21B984X-RAY DIFFRACTIONPOSITIONAL0.006
22G984X-RAY DIFFRACTIONPOSITIONAL0.006
23J984X-RAY DIFFRACTIONPOSITIONAL0.006
24O984X-RAY DIFFRACTIONPOSITIONAL0.007
31C1507X-RAY DIFFRACTIONPOSITIONAL0.124
32H1507X-RAY DIFFRACTIONPOSITIONAL0.124
33K1507X-RAY DIFFRACTIONPOSITIONAL0.113
34P1507X-RAY DIFFRACTIONPOSITIONAL0.127
41D243X-RAY DIFFRACTIONPOSITIONAL0.014
42E243X-RAY DIFFRACTIONPOSITIONAL0.014
43L243X-RAY DIFFRACTIONPOSITIONAL0.01
44M243X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.70.54861380.49492444258294
3.7-3.810.59731100.47032269237987
3.81-3.930.40511180.339626182736100
3.93-4.070.40021410.300126202761100
4.07-4.230.34771380.264326322770100
4.23-4.420.33841300.252626272757100
4.42-4.660.33651570.238826122769100
4.66-4.950.35491330.219626502783100
4.95-5.330.27581660.207826342800100
5.33-5.870.34141410.231226542795100
5.87-6.710.35991310.252926842815100
6.71-8.450.29791550.247226972852100
8.45-49.350.2411660.210228142980100
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)
1-0.50430.8041.2503-0.12261.11481.2711-0.4239-0.1029-0.3099-0.24991.6341-0.13780.9793-1.94010.01581.40880.01210.19981.3936-0.05661.376431.732117.9903-15.3152
20.59490.48041.61480.19080.88441.1832-0.1173-0.6696-0.12520.1460.47180.7107-1.33970.434801.49460.32270.16561.3572-0.04581.617831.260616.4316-15.4796
32.64060.1697-5.59271.58831.83714.9965-0.3152-0.61310.2404-0.1062-0.00480.07680.77330.01-0.00531.4874-0.221-0.01521.8661-0.06051.417-23.620426.9815-36.5917
47.288-1.2259-2.18282.62570.22012.39340.39751.29711.2877-0.9159-0.88-0.1229-0.49680.8473-0.00471.6603-0.2669-0.10631.40250.07961.688839.421130.8615-43.9901
50.93221.45840.82430.89960.39920.0726-0.4021-0.06211.0041-0.705-0.6603-0.296-2.1761-4.6885-0.00033.33260.7427-0.20373.2662-0.21871.888-8.014426.136-66.3781
60.1738-0.3212-0.22050.77990.89810.6725-0.1002-0.03560.8418-2.80431.1015-1.0182-1.60661.7355-0.11442.51230.2146-0.00682.3022-0.05032.0299-9.465426.4442-66.8795
77.18830.0299-2.67392.3523-1.91652.6658-0.1912-0.20150.69140.0745-0.0111-0.53030.56080.545301.71540.0069-0.051.3573-0.24071.544339.932834.61076.9525
88.99680.9867-0.8943.5168-3.5072.3210.57990.5356-0.5326-0.04270.05070.03031.0156-0.0226-0.00021.86490.094-0.04671.1161-0.07741.810733.0402-3.6603-35.2818
94.6214-0.0678-3.52242.8928-0.18161.72980.10870.4880.00880.1489-1.2649-0.3277-0.1491-0.54730.00021.2342-0.02680.08541.91230.01911.708810.01413.7277-47.5144
10-0.3641.26473.3917-2.1130.30320.77321.0914-1.56080.3299-0.2573-0.94980.3837-0.7123-0.2548-0.01732.6914-0.1813-0.26832.5973-0.79762.4833-25.35944.5785-84.2305
114.267-2.17551.92293.67961.4058.5835-0.3144-0.5398-1.43710.3158-0.14850.70340.6878-0.72440.00012.1786-0.34470.29942.1588-0.18351.737827.35521.052411.7416
120.3242-0.81731.98626.71263.78678.12160.49080.38160.4797-1.94740.1444-0.65-1.40340.51310.00022.44790.03620.05281.79730.00381.93558.238724.8464-92.4559
130.20670.48822.5717-1.05120.4624.25620.25940.04840.0284-0.1504-0.38680.1592-0.13540.0077-0.00011.2166-0.14910.12151.8867-0.20681.468258.817522.80441.2527
142.91111.5031-1.99834.54911.95942.6520.82330.0938-0.29260.4644-0.0554-0.41870.98130.4856-0.00021.95670.1481-0.15051.5891-0.19331.520753.8052-1.9455-26.2133
151.55810.517-1.13590.1891-0.3422-0.0648-0.5121-1.37340.32070.20390.3950.6179-2.20540.06420.00252.30360.5279-0.33142.36970.22282.4315-27.923926.8911-89.4498
164.6336-0.85650.12173.5381-1.5793.73910.29240.8613-0.7581-1.1535-0.07670.7988-0.7033-0.0780.00011.5579-0.2960.05191.2558-0.16041.9411-4.0607-2.0817-58.0914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 1 through 12)M1 - 12
2X-RAY DIFFRACTION2(chain 'L' and resid 15 through 26)L15 - 26
3X-RAY DIFFRACTION3(chain 'C' and resid 531 through 776)C531 - 776
4X-RAY DIFFRACTION4(chain 'K' and resid 531 through 776)K531 - 776
5X-RAY DIFFRACTION5(chain 'E' and resid 15 through 26)E15 - 26
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 12)D1 - 12
7X-RAY DIFFRACTION7(chain 'N' and resid 6 through 94)N6 - 94
8X-RAY DIFFRACTION8(chain 'I' and resid 5 through 91)I5 - 91
9X-RAY DIFFRACTION9(chain 'A' and resid 5 through 95)A5 - 95
10X-RAY DIFFRACTION10(chain 'G' and resid 224 through 358)G224 - 358
11X-RAY DIFFRACTION11(chain 'P' and resid 532 through 775)P532 - 775
12X-RAY DIFFRACTION12(chain 'H' and resid 531 through 776)H531 - 776
13X-RAY DIFFRACTION13(chain 'O' and resid 222 through 359)O222 - 359
14X-RAY DIFFRACTION14(chain 'J' and resid 223 through 361)J223 - 361
15X-RAY DIFFRACTION15(chain 'F' and resid 6 through 90)F6 - 90
16X-RAY DIFFRACTION16(chain 'B' and resid 229 through 358)B229 - 358

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