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- PDB-7f7i: Stapled Peptide Inhibitor in complex with PSD95 GK domain -

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Basic information

Entry
Database: PDB / ID: 7f7i
TitleStapled Peptide Inhibitor in complex with PSD95 GK domain
Components
  • ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
  • Disks large homolog 4
KeywordsPEPTIDE BINDING PROTEIN / MAGUK Stapled peptide entropy GK domain
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / embryo development / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / dendritic branch / neuron spine / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / juxtaparanode region of axon / frizzled binding / negative regulation of receptor internalization / dendritic spine organization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / positive regulation of excitatory postsynaptic potential / social behavior / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / beta-2 adrenergic receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / kinase binding / cell-cell adhesion / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / postsynapse / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsShang, Y. / Huang, X. / Li, X. / Zhang, M.
Funding support Hong Kong, 4items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17309616 Hong Kong
The University Grants Committee, Research Grants Council (RGC)T13-605/18-W Hong Kong
The University Grants Committee, Research Grants Council (RGC)AoE/M-09/12 Hong Kong
The University Grants Committee, Research Grants Council (RGC)AoE/P-705/16 Hong Kong
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain.
Authors: Unarta, I.C. / Xu, J. / Shang, Y. / Cheung, C.H.P. / Zhu, R. / Chen, X. / Cao, S. / Cheung, P.P. / Bierer, D. / Zhang, M. / Huang, X. / Li, X.
History
DepositionJun 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Disks large homolog 4
B: Disks large homolog 4
C: Disks large homolog 4
D: Disks large homolog 4
E: Disks large homolog 4
F: Disks large homolog 4
G: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
H: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
I: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
J: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
K: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2
L: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)151,29312
Polymers151,29312
Non-polymers00
Water6,846380
1
A: Disks large homolog 4
G: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-1 kcal/mol
Surface area10650 Å2
MethodPISA
2
B: Disks large homolog 4
H: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area11430 Å2
MethodPISA
3
C: Disks large homolog 4
I: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area10470 Å2
MethodPISA
4
D: Disks large homolog 4
J: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-3 kcal/mol
Surface area10550 Å2
MethodPISA
5
E: Disks large homolog 4
K: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-4 kcal/mol
Surface area10400 Å2
MethodPISA
6
F: Disks large homolog 4
L: ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Theoretical massNumber of molelcules
Total (without water)25,2152
Polymers25,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-3 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.029, 51.954, 144.500
Angle α, β, γ (deg.)91.780, 91.430, 120.970
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 533:551 or resseq 553:557 or (resid...
21(chain B and (resseq 533:551 or resseq 553:557 or (resid...
31(chain C and (resseq 533:551 or resseq 553:557 or (resid...
41(chain D and (resseq 533:551 or resseq 553:557 or (resid...
51(chain E and (resseq 533:551 or resseq 553:571 or resseq...
61(chain F and (resseq 533:551 or resseq 553:571 or resseq...
12(chain L and (resseq -6 or resseq -4 or (resid...
22(chain H and (resseq -6 or resseq -4 or (resid...
32(chain I and (resseq -6 or resseq -4 or (resid...
42(chain J and (resseq -6 or resseq -4 or (resid...
52(chain K and (resseq -6 or resseq -4 or (resid...

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
111TYRTYRLEULEU(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA533 - 55125 - 43
121SERSERASPASP(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA553 - 55745 - 49
131LYSLYSLYSLYS(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA55850
141HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
151HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
161HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
171HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
181HISHISGLYGLY(chain A and (resseq 533:551 or resseq 553:557 or (resid...AA532 - 71324 - 205
211TYRTYRLEULEU(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB533 - 55125 - 43
221SERSERASPASP(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB553 - 55745 - 49
231PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
241PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
251PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
261PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
271PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
281PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
291PHEPHEGLYGLY(chain B and (resseq 533:551 or resseq 553:557 or (resid...BB523 - 71315 - 205
311TYRTYRLEULEU(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC533 - 55125 - 43
321SERSERASPASP(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC553 - 55745 - 49
331LYSLYSLYSLYS(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC55850
341HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
351HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
361HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
371HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
381HISHISGLYGLY(chain C and (resseq 533:551 or resseq 553:557 or (resid...CC532 - 71324 - 205
411TYRTYRLEULEU(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD533 - 55125 - 43
421SERSERASPASP(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD553 - 55745 - 49
431HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
441HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
451HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
461HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
471HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
481HISHISGLYGLY(chain D and (resseq 533:551 or resseq 553:557 or (resid...DD532 - 71324 - 205
511TYRTYRLEULEU(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE533 - 55125 - 43
521SERSERARGARG(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE553 - 57145 - 63
531TYRTYRGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE573 - 57765 - 69
541LYSLYSGLUGLU(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE588 - 59080 - 82
551ALAALAILEILE(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE595 - 59387 - 85
561PHEPHESERSER(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE598 - 69690 - 188
571HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
581ASNASNASNASN(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE60597
591HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5101HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5111HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5121HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5131HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
5141HISHISGLYGLY(chain E and (resseq 533:551 or resseq 553:571 or resseq...EE532 - 71324 - 205
611TYRTYRLEULEU(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF533 - 55125 - 43
621SERSERARGARG(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF553 - 57145 - 63
631TYRTYRGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF573 - 57765 - 69
641ASPASPARGARG(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF579 - 58671 - 78
651ALAALAILEILE(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF595 - 59387 - 85
661PHEPHESERSER(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF598 - 60690 - 98
671HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
681ASNASNASNASN(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF60597
691HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6101HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6111HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6121HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
6131HISHISGLYGLY(chain F and (resseq 533:551 or resseq 553:571 or resseq...FF532 - 71324 - 205
112ACEACEACEACE(chain L and (resseq -6 or resseq -4 or (resid...LL-61
122ILEILEILEILE(chain L and (resseq -6 or resseq -4 or (resid...LL-43
132ARGARGARGARG(chain L and (resseq -6 or resseq -4 or (resid...LL-34
142ACEACENH2NH2(chain L and (resseq -6 or resseq -4 or (resid...LL-6 - 71 - 14
212ACEACEACEACE(chain H and (resseq -6 or resseq -4 or (resid...HH-61
222ILEILEILEILE(chain H and (resseq -6 or resseq -4 or (resid...HH-43
232ARGARGARGARG(chain H and (resseq -6 or resseq -4 or (resid...HH-34
242ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
252ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
262ACEACENH2NH2(chain H and (resseq -6 or resseq -4 or (resid...HH-6 - 71 - 14
312ACEACEACEACE(chain I and (resseq -6 or resseq -4 or (resid...II-61
322ILEILEILEILE(chain I and (resseq -6 or resseq -4 or (resid...II-43
332ARGARGARGARG(chain I and (resseq -6 or resseq -4 or (resid...II-34
342ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
352ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
362ACEACENH2NH2(chain I and (resseq -6 or resseq -4 or (resid...II-6 - 71 - 14
412ACEACEACEACE(chain J and (resseq -6 or resseq -4 or (resid...JJ-61
422ILEILEILEILE(chain J and (resseq -6 or resseq -4 or (resid...JJ-43
432ARGARGARGARG(chain J and (resseq -6 or resseq -4 or (resid...JJ-34
442ACEACENH2NH2(chain J and (resseq -6 or resseq -4 or (resid...JJ-6 - 71 - 14
512ACEACEACEACE(chain K and (resseq -6 or resseq -4 or (resid...KK-61
522ILEILEILEILE(chain K and (resseq -6 or resseq -4 or (resid...KK-43
532ARGARGARGARG(chain K and (resseq -6 or resseq -4 or (resid...KK-34
542ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14
552ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14
562ACEACENH2NH2(chain K and (resseq -6 or resseq -4 or (resid...KK-6 - 71 - 14

NCS ensembles :
ID
1
2

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Components

#1: Protein
Disks large homolog 4


Mass: 23611.574 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31016
#2: Protein/peptide
ACE-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYZ-ALA-ILE-GLN-NH2


Mass: 1603.869 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 35 % w/v PEP 629, 100 mM HEPES (pH7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97799 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97799 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.07
ReflectionResolution: 2.595→50 Å / Num. obs: 37969 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.087 / Rrim(I) all: 0.171 / Χ2: 1.195 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.70.69418930.6320.4170.8111.0997.1
2.64-2.693.70.60419370.710.3630.7061.13197
2.69-2.743.60.57618680.7390.3450.6721.02397.2
2.74-2.83.70.50519090.7670.3020.5891.10197
2.8-2.863.60.46218990.7670.2780.541.0996.9
2.86-2.933.70.4218410.8390.2520.491.13196.7
2.93-33.70.31819500.9060.1910.3721.20996.8
3-3.083.70.28818540.9110.1720.3361.12996.6
3.08-3.173.70.25419270.9260.1520.2961.24696.7
3.17-3.283.70.21718350.9430.1290.2531.1996
3.28-3.393.70.17919070.9550.1070.2081.23396.4
3.39-3.533.70.15618360.9690.0930.1811.22695.7
3.53-3.693.70.1419010.9710.0840.1631.29395.1
3.69-3.883.70.1117990.980.0660.1281.30392.7
3.88-4.133.90.09418990.9890.0550.1091.25899.2
4.13-4.453.90.08219410.990.0480.0961.29399.2
4.45-4.893.90.07819390.9890.0460.091.17899.3
4.89-5.640.08519730.990.0490.0981.20299.4
5.6-7.0540.08719180.9920.0510.1011.2199.6
7.05-503.90.05519430.9950.0320.0641.32998.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UAT

3uat


Resolution: 2.595→33.523 Å / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2624 1987 5.23 %
Rwork0.2142 36038 -
obs0.2167 37969 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145 Å2 / Biso mean: 48.8892 Å2 / Biso min: 7 Å2
Refinement stepCycle: final / Resolution: 2.595→33.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9422 0 0 380 9802
Biso mean---37.22 -
Num. residues----1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089605
X-RAY DIFFRACTIONf_angle_d1.22512958
X-RAY DIFFRACTIONf_chiral_restr0.0641412
X-RAY DIFFRACTIONf_plane_restr0.011718
X-RAY DIFFRACTIONf_dihedral_angle_d28.1643600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4000X-RAY DIFFRACTION16.388TORSIONAL
12B4000X-RAY DIFFRACTION16.388TORSIONAL
13C4000X-RAY DIFFRACTION16.388TORSIONAL
14D4000X-RAY DIFFRACTION16.388TORSIONAL
15E4000X-RAY DIFFRACTION16.388TORSIONAL
16F4000X-RAY DIFFRACTION16.388TORSIONAL
21L173X-RAY DIFFRACTION16.388TORSIONAL
22H173X-RAY DIFFRACTION16.388TORSIONAL
23I173X-RAY DIFFRACTION16.388TORSIONAL
24J173X-RAY DIFFRACTION16.388TORSIONAL
25K173X-RAY DIFFRACTION16.388TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5988-2.66380.35021450.2784249689
2.6638-2.73570.3461670.2775254591
2.7357-2.81620.28961310.2562258392
2.8162-2.90710.3361340.2628255292
2.9071-3.01090.25331230.2484260192
3.0109-3.13140.30741360.2397254792
3.1314-3.27380.29171280.2261254792
3.2738-3.44620.25361230.206260592
3.4462-3.66190.25131320.2006252791
3.6619-3.94420.26571150.1904250490
3.9442-4.34040.22511370.1795264394
4.3404-4.96670.22721360.1764262194
4.9667-6.25090.22741580.2199263094
6.2509-33.5230.241420.2057263795
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)
13.7458-1.26171.30813.3918-0.35179.0675-0.0048-0.1511-1.06470.57460.35290.5730.0769-0.455-0.31650.19380.00160.03670.28310.01430.491618.602719.4869-10.9583
23.37170.9566-2.17212.11390.84955.59330.1482-0.37290.01780.1539-0.027-0.2725-0.44980.5565-0.1620.2882-0.0407-0.05630.3169-0.02040.257821.277832.93870.6848
35.6194-1.74371.92566.0398-2.36684.9514-0.0205-0.0206-0.1607-0.31330.06620.1157-0.3860.3035-0.04520.2989-0.06090.07570.1641-0.0410.200920.053524.7211-24.2238
40.9647-0.22961.08150.92370.370.93970.0346-0.0446-0.1358-0.0285-0.0316-0.0019-0.2345-0.02740.00240.4142-0.0480.01390.17610.0330.34937.443536.4721-53.3749
53.8299-0.6398-1.37750.23870.39683.76290.1691-0.3364-0.45530.1108-0.203-0.35160.53260.17880.04910.3965-0.0352-0.05740.18550.09040.328820.371428.1284-43.8018
68.3015-0.96051.49040.1574-0.39930.36830.3037-0.26470.0928-0.2682-0.18270.0330.2747-0.1013-0.06150.4412-0.03770.01760.2140.07070.239210.194731.831-50.5687
74.35381.8639-2.87453.5252-2.63684.2152-0.03570.0901-0.02590.19350.16730.14340.30960.2646-0.19160.3324-0.0257-0.02230.1784-0.09290.26588.59527.0242-64.3904
85.5531-0.6367-1.28711.1992-0.73484.10830.09110.38020.0458-0.2064-0.1033-0.16770.14630.39920.01660.5088-0.04610.02440.2604-0.02340.25412.042634.8827-73.5273
92.57780.12991.40060.2297-0.91135.09610.1840.1095-0.07120.0309-0.1388-0.18090.21560.59570.00510.33080.019-0.02450.17550.01740.427-0.087413.8834-48.4683
107.15086.0289-5.74348.8973-5.19995.3486-0.21510.70020.1929-0.54510.37720.57780.1467-0.311-0.12290.43410.0111-0.07560.2791-0.02530.1663-13.65322.6704-66.8113
112.33530.34880.17272.0214-1.17543.0337-0.0024-0.3414-0.1259-0.5123-0.04360.56040.159-0.21330.05250.2727-0.078-0.07680.2421-0.01760.3726-14.198516.6166-58.9397
122.20471.37230.9222.12642.19036.45660.016-0.18970.1393-0.0325-0.20230.1485-0.0565-0.490.17070.2345-0.01310.02150.15810.04020.3471-6.39814.1822-37.9009
132.7249-1.69381.4912.92841.64675.0852-0.3450.34770.4230.18130.0940.14240.0427-0.59420.22670.1768-0.04430.03510.3275-0.00880.4326-6.980525.37670.5817
142.960.72572.86963.510.94424.22110.17060.1887-0.3762-0.06030.0107-0.20260.30430.1526-0.17170.2493-0.01890.07080.2165-0.05050.3074-5.107410.7704-15.4885
154.58672.1871-2.93244.222-1.01548.907-0.1958-0.2758-0.4470.37940.2765-0.23860.6924-0.0041-0.0630.46880.0069-0.09330.20240.01350.2808-3.374915.67559.2191
168.7521-0.3623-2.37646.9239-3.05274.8180.17690.02410.04150.65590.33420.3118-0.3060.1107-0.5060.2868-0.0713-0.03650.2644-0.03950.2721-3.409627.720211.8179
177.47051.3596-2.7612.2943-0.32595.72620.010.0219-0.8443-0.2167-0.018-0.63560.58090.34580.0370.47370.0580.02870.299-0.00030.532-16.69154.16347.8976
182.4435-2.2972-1.88676.9265.79644.8005-0.0463-0.32050.3774-1.6828-0.2025-0.29950.53060.59610.14720.94070.19630.16910.38460.19030.26960.18675.722127.8623
199.07750.27881.93480.1806-0.94245.9090.15170.54910.1090.3512-0.0209-0.0086-0.32620.1355-0.13920.5995-0.10930.02270.2602-0.00540.3771-3.362815.711532.8888
206.48692.7114-4.81431.5203-1.43054.3324-0.00820.73280.518-0.37270.13310.1913-0.1248-0.2203-0.07750.63180.0127-0.03720.28320.05190.2759-11.872113.818135.8973
214.84180.8143-0.57372.8061-1.50138.15750.1421-0.45350.16920.760.0532-0.1445-0.904-0.1226-0.22310.7668-0.05570.04210.33860.08550.3775-15.607614.029550.1282
224.97892.4887-3.48443.3151-2.8332.86720.2439-1.298-0.2670.7004-0.7764-0.5673-0.84261.16540.4881.3337-0.043-0.15460.90220.00870.5049-8.130210.055863.3297
231.9987-3.8141-2.77418.8976.30294.6030.1511-0.4793-0.5439-0.65430.1109-0.14270.8692-0.4756-0.27870.59370.01950.04890.38970.16870.4491-22.78634.303757.8166
241.60281.1089-2.63243.8587-4.27977.9282-0.313-0.1345-0.1629-0.1615-0.0907-0.11150.54620.21780.40040.54540.03790.0630.25230.01940.392524.220726.319142.46
258.2027-1.95680.53595.66111.68354.68680.3956-0.5881-0.17550.3004-0.63580.54360.3769-0.13570.23470.6339-0.02370.12690.28360.03010.30911.504623.785954.8931
265.80276.2744-3.26228.8083-4.72015.46510.0324-0.4510.103-0.11320.0344-0.0074-0.3871-0.2369-0.09050.27840.10070.04080.3403-0.04960.303413.067627.484147.9415
274.24971.8170.90181.12221.68037.99730.0317-0.32550.22210.067-0.24120.6146-0.4402-0.46460.19060.64510.06650.06080.2460.05210.52216.629334.290237.0028
283.9061-3.5185-1.63137.71031.39722.06820.29110.9317-0.9937-1.002-0.98520.76340.7102-1.35990.63071.304-0.1049-0.10611.0218-0.39520.764116.570723.219820.7014
297.3389-4.7705-4.10313.96912.62822.6070.06080.3058-0.1496-1.2454-0.1939-0.4545-0.32120.47310.18951.0807-0.01050.15620.42760.01530.370127.270334.499725.5335
303.64533.83894.83824.06875.12316.4071-0.1328-0.5849-0.4589-0.1876-1.15140.9227-0.50030.27360.99580.4301-0.03910.00840.39520.08630.43910.383331.2313-4.69
311.9601-0.1862-0.69412.6242-4.02846.74920.29870.23570.0359-2.1360.1407-0.54820.1666-0.8024-0.40760.583-0.01510.13560.26110.01690.391813.546338.0188-6.6402
322.01151.3855-1.70762.1012-0.49851.8021-0.58840.82121.2287-0.98180.24870.3386-0.1467-0.9058-0.05360.9131-0.041-0.18020.55930.33720.586420.30839.5016-51.5567
338.6277-1.86624.68111.4361.60589.36120.30241.10330.8286-0.8513-0.0740.324-0.340.8462-0.11290.4514-0.02230.06890.12360.02880.42524.736433.4973-54.5165
346.6116-3.77550.19965.27231.95341.3549-0.508-0.3269-0.73930.4241.7886-0.0076-0.2361-0.6061-0.54660.7732-0.06520.12330.30.19270.5475-6.687126.7007-54.9061
359.84844.4001-3.74274.2161-4.38766.91960.1784-0.8353-0.58110.6142-0.10730.0452-0.78390.8293-0.09140.3933-0.18040.09410.41850.0350.275-14.194527.3589-52.6848
365.92964.4193.66278.35176.55158.107-0.4996-0.54811.8123-0.649-0.95130.5577-2.4649-0.1431.35230.70450.0032-0.13980.4118-0.05440.8392-13.868914.5038-6.3282
375.20016.15491.65167.29982.04322.0477-0.3808-0.938-0.35522.1512-0.1779-0.07280.4564-0.34810.03711.0250.05760.1729-0.7669-0.39880.3468-10.79567.0318-5.0332
381.25480.98430.92584.834-3.0414.0681-0.25430.0059-0.62681.7807-0.03521.5243-0.3191-0.06850.18831.12070.27820.14030.54250.10131.0108-2.9893.880340.9497
398.2655-5.5429-3.30043.77882.84332.01140.9707-0.94390.51240.7550.677-0.4311-0.6105-0.3921-1.25860.9473-0.12240.0280.38710.02450.43451.313910.119643.246
400.7879-0.53511.25110.323-0.83962.0515-0.43420.55110.4389-0.1767-0.53660.4258-0.98132.1005-0.21540.8241-0.13220.52861.0814-0.15220.875220.330418.11243.45
414.58124.49832.83244.45212.26437.3004-0.47421.4986-0.1263-0.57090.2737-0.08070.93080.75540.28190.36260.02960.02510.4079-0.06910.612.902416.955241.4892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 532 through 564 )A532 - 564
2X-RAY DIFFRACTION2chain 'A' and (resid 565 through 640 )A565 - 640
3X-RAY DIFFRACTION3chain 'A' and (resid 641 through 713 )A641 - 713
4X-RAY DIFFRACTION4chain 'B' and (resid 523 through 573 )B523 - 573
5X-RAY DIFFRACTION5chain 'B' and (resid 574 through 606 )B574 - 606
6X-RAY DIFFRACTION6chain 'B' and (resid 607 through 631 )B607 - 631
7X-RAY DIFFRACTION7chain 'B' and (resid 632 through 654 )B632 - 654
8X-RAY DIFFRACTION8chain 'B' and (resid 655 through 713 )B655 - 713
9X-RAY DIFFRACTION9chain 'C' and (resid 532 through 564 )C532 - 564
10X-RAY DIFFRACTION10chain 'C' and (resid 565 through 594 )C565 - 594
11X-RAY DIFFRACTION11chain 'C' and (resid 595 through 622 )C595 - 622
12X-RAY DIFFRACTION12chain 'C' and (resid 623 through 713 )C623 - 713
13X-RAY DIFFRACTION13chain 'D' and (resid 532 through 563 )D532 - 563
14X-RAY DIFFRACTION14chain 'D' and (resid 564 through 621 )D564 - 621
15X-RAY DIFFRACTION15chain 'D' and (resid 622 through 687 )D622 - 687
16X-RAY DIFFRACTION16chain 'D' and (resid 688 through 713 )D688 - 713
17X-RAY DIFFRACTION17chain 'E' and (resid 532 through 564 )E532 - 564
18X-RAY DIFFRACTION18chain 'E' and (resid 565 through 574 )E565 - 574
19X-RAY DIFFRACTION19chain 'E' and (resid 575 through 606 )E575 - 606
20X-RAY DIFFRACTION20chain 'E' and (resid 607 through 621 )E607 - 621
21X-RAY DIFFRACTION21chain 'E' and (resid 622 through 654 )E622 - 654
22X-RAY DIFFRACTION22chain 'E' and (resid 655 through 696 )E655 - 696
23X-RAY DIFFRACTION23chain 'E' and (resid 697 through 713 )E697 - 713
24X-RAY DIFFRACTION24chain 'F' and (resid 532 through 574 )F532 - 574
25X-RAY DIFFRACTION25chain 'F' and (resid 575 through 594 )F575 - 594
26X-RAY DIFFRACTION26chain 'F' and (resid 595 through 622 )F595 - 622
27X-RAY DIFFRACTION27chain 'F' and (resid 623 through 650 )F623 - 650
28X-RAY DIFFRACTION28chain 'F' and (resid 651 through 687 )F651 - 687
29X-RAY DIFFRACTION29chain 'F' and (resid 688 through 713 )F688 - 713
30X-RAY DIFFRACTION30chain 'G' and (resid -6 through 0 )G-6 - 0
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 7 )G1 - 7
32X-RAY DIFFRACTION32chain 'H' and (resid -6 through 0 )H-6 - 0
33X-RAY DIFFRACTION33chain 'H' and (resid 1 through 7 )H1 - 7
34X-RAY DIFFRACTION34chain 'I' and (resid -6 through 0 )I-6 - 0
35X-RAY DIFFRACTION35chain 'I' and (resid 1 through 7 )I1 - 7
36X-RAY DIFFRACTION36chain 'J' and (resid -6 through 0 )J-6 - 0
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 7 )J1 - 7
38X-RAY DIFFRACTION38chain 'K' and (resid -6 through 0 )K-6 - 0
39X-RAY DIFFRACTION39chain 'K' and (resid 1 through 7 )K1 - 7
40X-RAY DIFFRACTION40chain 'L' and (resid -6 through 0 )L-6 - 0
41X-RAY DIFFRACTION41chain 'L' and (resid 1 through 7 )L1 - 7

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