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- PDB-7doc: Crystal structure of Zika NS2B-NS3 protease with compound 5 -

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Basic information

Entry
Database: PDB / ID: 7doc
TitleCrystal structure of Zika NS2B-NS3 protease with compound 5
Components
  • (Core protein) x 4
  • (Genome polyprotein) x 2
  • 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / Viral protease / Protease inhibitor complex
Function / homology
Function and homology information


symbiont-mediated suppression of host interferon-mediated signaling pathway / : / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host interferon-mediated signaling pathway / : / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsQuek, J.P.
Funding support Singapore, 3items
OrganizationGrant numberCountry
Other governmentStart up grant Singapore
Other governmentCBRG15May045 Singapore
Other governmentNRF2016NRF-CRP001-063 Singapore
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: 2-Cyanoisonicotinamide Conjugation: A Facile Approach to Generate Potent Peptide Inhibitors of the Zika Virus Protease.
Authors: Patil, N.A. / Quek, J.P. / Schroeder, B. / Morewood, R. / Rademann, J. / Luo, D. / Nitsche, C.
History
DepositionDec 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core protein
B: Core protein
C: Genome polyprotein
D: Core protein
E: Serine protease subunit NS2B
F: Core protein
G: Core protein
H: Genome polyprotein
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Theoretical massNumber of molelcules
Total (without water)83,9579
Polymers83,9579
Non-polymers00
Water6,684371
1
A: Core protein
B: Core protein


Theoretical massNumber of molelcules
Total (without water)20,6902
Polymers20,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area8850 Å2
MethodPISA
2
C: Genome polyprotein
D: Core protein


Theoretical massNumber of molelcules
Total (without water)20,4322
Polymers20,4322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area8390 Å2
MethodPISA
3
E: Serine protease subunit NS2B
F: Core protein


Theoretical massNumber of molelcules
Total (without water)21,3062
Polymers21,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area9150 Å2
MethodPISA
4
G: Core protein
H: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)20,7182
Polymers20,7182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area8930 Å2
MethodPISA
5
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


  • defined by author&software
  • 810 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8101
Polymers8101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.154, 59.614, 215.073
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
11(chain A and (resid 51 through 61 or (resid 62...
21(chain C and (resid 51 through 65 or (resid 66...
31(chain E and (resid 51 through 61 or (resid 62...
41(chain G and (resid 51 through 61 or (resid 62...
12(chain B and (resid 18 through 29 or (resid 30...
22(chain D and (resid 18 through 30 or resid 34...
32(chain F and (resid 18 through 60 or (resid 64...
42(chain H and (resid 18 through 30 or resid 34...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 51 through 61 or (resid 62...A51 - 61
121(chain A and (resid 51 through 61 or (resid 62...A62 - 66
131(chain A and (resid 51 through 61 or (resid 62...A50 - 88
141(chain A and (resid 51 through 61 or (resid 62...A50 - 88
151(chain A and (resid 51 through 61 or (resid 62...A50 - 88
161(chain A and (resid 51 through 61 or (resid 62...A50 - 88
171(chain A and (resid 51 through 61 or (resid 62...A73
181(chain A and (resid 51 through 61 or (resid 62...A50 - 88
191(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1101(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1111(chain A and (resid 51 through 61 or (resid 62...A50 - 88
211(chain C and (resid 51 through 65 or (resid 66...C51 - 65
221(chain C and (resid 51 through 65 or (resid 66...C66
231(chain C and (resid 51 through 65 or (resid 66...C50 - 87
241(chain C and (resid 51 through 65 or (resid 66...C50 - 87
251(chain C and (resid 51 through 65 or (resid 66...C50 - 87
261(chain C and (resid 51 through 65 or (resid 66...C50 - 87
311(chain E and (resid 51 through 61 or (resid 62...E51 - 61
321(chain E and (resid 51 through 61 or (resid 62...E62 - 66
331(chain E and (resid 51 through 61 or (resid 62...E51 - 89
341(chain E and (resid 51 through 61 or (resid 62...E51 - 89
351(chain E and (resid 51 through 61 or (resid 62...E51 - 89
361(chain E and (resid 51 through 61 or (resid 62...E51 - 89
411(chain G and (resid 51 through 61 or (resid 62...G51 - 61
421(chain G and (resid 51 through 61 or (resid 62...G62 - 66
431(chain G and (resid 51 through 61 or (resid 62...G50 - 88
441(chain G and (resid 51 through 61 or (resid 62...G50 - 88
451(chain G and (resid 51 through 61 or (resid 62...G50 - 88
461(chain G and (resid 51 through 61 or (resid 62...G50 - 88
112(chain B and (resid 18 through 29 or (resid 30...B18 - 29
122(chain B and (resid 18 through 29 or (resid 30...B30
132(chain B and (resid 18 through 29 or (resid 30...B17 - 169
142(chain B and (resid 18 through 29 or (resid 30...B17 - 169
152(chain B and (resid 18 through 29 or (resid 30...B17 - 169
162(chain B and (resid 18 through 29 or (resid 30...B17 - 169
212(chain D and (resid 18 through 30 or resid 34...D18 - 30
222(chain D and (resid 18 through 30 or resid 34...D34 - 53
232(chain D and (resid 18 through 30 or resid 34...D54
242(chain D and (resid 18 through 30 or resid 34...D18 - 169
252(chain D and (resid 18 through 30 or resid 34...D0
262(chain D and (resid 18 through 30 or resid 34...D64 - 65
272(chain D and (resid 18 through 30 or resid 34...D18 - 169
282(chain D and (resid 18 through 30 or resid 34...D18 - 169
292(chain D and (resid 18 through 30 or resid 34...D18 - 169
2102(chain D and (resid 18 through 30 or resid 34...D18 - 169
312(chain F and (resid 18 through 60 or (resid 64...F18 - 60
322(chain F and (resid 18 through 60 or (resid 64...F64 - 65
332(chain F and (resid 18 through 60 or (resid 64...F14 - 171
342(chain F and (resid 18 through 60 or (resid 64...F14 - 171
352(chain F and (resid 18 through 60 or (resid 64...F14 - 171
362(chain F and (resid 18 through 60 or (resid 64...F14 - 171
412(chain H and (resid 18 through 30 or resid 34...H18 - 30
422(chain H and (resid 18 through 30 or resid 34...H34 - 53
432(chain H and (resid 18 through 30 or resid 34...H54
442(chain H and (resid 18 through 30 or resid 34...H18 - 170
452(chain H and (resid 18 through 30 or resid 34...H18 - 170
462(chain H and (resid 18 through 30 or resid 34...H18 - 170
472(chain H and (resid 18 through 30 or resid 34...H18 - 170

NCS ensembles :
ID
1
2

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Components

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Protein/peptide , 4 types, 5 molecules AGCEI

#1: Protein/peptide Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 4347.659 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_72127gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2R4LVW1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Protein/peptide Genome polyprotein


Mass: 4218.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#5: Protein/peptide Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 4361.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1
#8: Protein/peptide 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Mass: 809.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 4 types, 4 molecules BDFH

#2: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16342.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16213.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#6: Protein Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16944.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#7: Protein Genome polyprotein / NS3 Protease


Mass: 16370.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX12

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Non-polymers , 1 types, 371 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate Trihydrate pH 4.6, 30% Peg 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.15
ReflectionResolution: 1.904→45.63 Å / Num. obs: 60261 / % possible obs: 99.39 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1312 / Rpim(I) all: 0.03716 / Rrim(I) all: 0.1365 / Net I/σ(I): 12.2
Reflection shellResolution: 1.904→1.972 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.8121 / Num. unique obs: 5640 / CC1/2: 0.925 / Rpim(I) all: 0.2344 / Rrim(I) all: 0.8459 / % possible all: 94.08

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.904→45.63 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2286 2981 4.97 %
Rwork0.2092 57210 -
obs-60243 99.4 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.19 Å2 / Biso mean: 45.9095 Å2 / Biso min: 23.6 Å2
Refinement stepCycle: final / Resolution: 1.904→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 104 371 5976
Biso mean--73.4 50.76 -
Num. residues----765
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A436X-RAY DIFFRACTION3.48TORSIONAL
12C436X-RAY DIFFRACTION3.48TORSIONAL
13E436X-RAY DIFFRACTION3.48TORSIONAL
14G436X-RAY DIFFRACTION3.48TORSIONAL
21B1720X-RAY DIFFRACTION3.48TORSIONAL
22D1720X-RAY DIFFRACTION3.48TORSIONAL
23F1720X-RAY DIFFRACTION3.48TORSIONAL
24H1720X-RAY DIFFRACTION3.48TORSIONAL
LS refinement shellResolution: 1.904→1.972 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.275 281
Rwork0.2947 5630
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)
15.33740.96372.74063.0533-1.10522.30530.0897-0.76831.0930.8508-0.08550.9012-0.6763-0.3187-0.08830.58330.08780.14340.6624-0.04730.3915-8.9807-0.538240.233
23.7946-2.14351.59637.6238-2.17790.92370.14890.3016-0.09960.8049-0.4879-0.6483-1.1144-0.21780.23370.73220.026-0.0630.51520.03170.29711.7774-5.277150.4588
33.6973-0.41364.7570.0983-0.36716.57040.0546-1.33490.09221.7733-0.37720.3565-0.13150.36820.14691.3447-0.0182-0.02890.73910.04660.21151.4756-18.134459.323
46.0150.58951.41958.8221-0.89880.45570.19740.1550.18920.7228-0.01520.6331-0.12281.0276-0.29191.0056-0.0817-0.00850.73050.13290.3013-4.6179-33.63950.0877
53.3549-1.05291.83141.6975-1.70822.7236-0.22940.0424-0.3494-0.71670.2193-0.00880.47690.05060.05960.646-0.15990.05860.7348-0.02440.229-9.8242-30.357935.3695
65.5518-0.3859-0.81311.57-1.04733.0567-0.25180.16250.67230.10730.26370.1479-0.6161-0.1985-0.10960.55760.04750.01470.5499-0.06590.2253-6.6541-4.410643.4568
73.54020.3518-0.75141.86070.0872.9665-0.27490.0105-0.1382-0.11680.180.1283-0.2931-0.18710.13480.5304-0.02430.03540.5252-0.03130.1237-2.6572-10.77736.9924
81.9714-1.92580.79056.5808-0.16563.8495-0.09520.15190.0917-0.56110.27940.4977-0.841-0.2364-0.23520.54590.00440.01270.620.06630.2817-3.0755-5.226732.3258
92.8312.3718-0.7286.87081.49552.7543-0.0881-0.5368-0.1624-0.4656-0.0691-0.5108-0.0188-0.26540.09190.47770.01530.00730.51010.02770.1454-3.2628-15.783933.0385
101.4940.31270.63511.855-1.29523.24630.2002-0.2789-0.19830.6485-0.1363-0.3897-0.35040.5457-0.13140.5499-0.0278-0.04730.6108-0.00070.23266.635-19.522342.9962
110.68931.1998-0.26962.5260.24611.29510.0593-0.2353-0.06971.0951-0.11850.27950.3518-0.0357-0.04470.6643-0.07890.01130.58880.03670.2172-4.7422-20.722849.3484
129.34542.76524.60826.8980.75142.83920.5275-0.5809-0.63750.87720.3807-0.95970.89980.1638-0.79760.7080.0842-0.09650.6088-0.0620.31745.8049-17.017649.4497
131.3165-0.00040.56761.69160.74981.00950.1311-0.15640.2410.1035-0.07930.30380.5208-0.42490.02370.6755-0.00680.0330.66430.05260.1511-6.411-23.611144.5574
144.7986-1.2037-1.00058.52862.08579.07731.315-0.31580.53870.9119-0.4274-1.1377-2.10471.7723-0.21440.8999-0.42970.08820.9360.05210.4483-21.6570.488267.9924
150.15380.480.01382.122-0.92031.58280.13060.8453-0.0939-0.8921-0.3022-0.37380.10150.34970.09660.62550.08540.00160.9918-0.10850.3141-29.2433-17.38652.9269
162.341-1.8516-1.28013.4144-0.07771.3199-0.06740.2288-0.25050.12650.15440.05570.29260.1041-0.13520.58440.1799-0.07080.9354-0.07820.2745-20.9285-28.670372.5636
173.99171.87132.42191.67941.64766.3914-0.5846-0.21260.2614-0.23560.11740.204-0.7599-0.04830.20550.6097-0.01720.01970.63610.13520.1833-27.4291-2.632963.3992
182.0023-1.8366-0.86212.781-0.57693.8823-0.6894-0.63760.80590.2510.3549-0.9212-0.20290.8160.41040.62460.0997-0.05980.88030.0662-0.0537-21.0658-4.667565.4663
193.2554-0.7251-1.10583.15760.65883.6124-0.44580.15720.00470.07060.2395-0.2241-0.55670.870.1840.4312-0.03190.01920.57110.00330.1517-28.484-9.696970.8864
201.8321-0.1719-0.93064.74840.84680.8721-0.221-0.02010.453-0.12180.4143-0.7654-0.59920.2892-0.24630.5786-0.1122-0.0270.7089-0.02040.1914-28.4748-4.248175.5968
211.9554-1.85360.81066.3052-1.20892.845-0.09860.0561-0.0906-0.15170.40710.16280.19560.4221-0.41750.46170.02750.02490.5445-0.00390.1545-28.1355-14.716874.8488
221.7561-0.16360.4966.17594.22324.9039-0.13150.3509-0.20330.13710.02920.1490.2528-0.1786-0.00770.4618-0.01430.00410.6128-0.02870.1878-37.4005-18.3164.6663
231.21540.4908-0.47412.91240.76750.5466-0.12590.2822-0.0163-0.64530.1896-0.1953-0.08690.116-0.06230.55670.10440.0590.7565-0.03910.2346-26.3259-18.846156.4561
242.03390.07790.21792.4123-0.74781.75380.23030.336-0.4533-0.1788-0.1562-0.07680.13760.676-0.01140.56750.04760.02320.7724-0.070.1836-25.9751-20.976362.2831
255.78162.3233-0.71158.89093.27188.81680.32480.51280.6372-0.28440.48240.6661-0.5479-1.4217-0.37280.3445-0.04490.01640.85570.23140.4123-15.1058-9.35310.9148
265.8241-1.70724.14165.24790.72274.09920.31960.4165-0.0945-1.63930.0558-0.06880.2110.2097-0.22930.4001-0.0519-0.02310.55660.09210.2165-8.4859-18.68982.0703
274.95033.597-2.35873.0428-1.4071.5889-0.59320.99890.727-1.59850.38870.3535-0.0119-0.1123-0.00890.57320.0134-0.02750.77080.04560.33513.9246-15.3502-5.6298
285.3391-1.8502-0.918.61153.99828.26150.22530.116-0.06990.2194-0.2984-1.241-0.43180.20420.16860.4325-0.02950.03390.610.17820.42618.0673-8.3016.2523
292.7871-1.9563-0.3671.61210.32020.06890.3198-0.80310.11270.6545-0.224-0.0286-0.27820.40620.12620.7286-0.2175-0.03120.61430.01640.221510.915-4.876220.9767
303.1427-1.3826-0.50049.59462.89259.22650.0557-0.19140.7998-0.20160.7061-1.299-0.23611.2679-0.72010.5388-0.11620.05830.5701-0.07250.425418.4245-1.751314.0336
310.92582.0774-0.59339.6378-1.17920.38330.02440.59930.127-0.0199-0.02231.03640.04960.03810.10040.4040.0436-0.02180.61620.06050.3017-14.4653-19.2089.9103
322.54160.09312.06898.9896-1.81142.06610.0747-0.01390.58670.4551-0.65150.4931-0.0992-0.49460.48660.44340.0030.07930.704-0.02820.1113-10.1815-7.572911.7064
332.16160.4737-1.59051.8193-0.23112.22360.1613-0.01470.05560.2958-0.12130.1495-0.0466-0.1871-0.04230.4159-0.0173-0.00660.43470.0220.1343-2.9088-15.352617.2889
342.83511.776-0.77542.6155-0.7160.2997-0.07340.039-0.043-0.04750.0535-0.0548-0.00480.06090.03130.3422-0.00350.00440.44340.0420.14734.8536-11.4416.2804
354.103-0.47930.13892.15261.84682.7070.14090.07430.0216-0.2815-0.05110.4847-0.0166-0.5983-0.04020.3743-0.036-0.01990.45370.09080.2285-38.1364-40.21987.7478
363.1521.78250.10534.38971.790.8676-0.73311.91210.1342-1.9580.41550.44260.0725-0.35280.34220.78290.07360.0290.77920.00560.1951-21.8131-46.4875-4.9393
372.00160.73289.63425.61683.16842.0009-0.6827-0.22190.6665-0.2101-0.5789-0.1096-0.1988-0.17130.40170.4233-0.10420.07330.6111-0.04610.1829-7.4858-38.88785.1926
380.1213-0.43170.62763.3279-1.86083.31130.3921-0.80360.01570.361-0.4047-0.1953-0.14780.9015-0.00040.5779-0.1543-0.01210.57560.00840.1973-10.6369-34.703819.551
393.38432.522-0.36356.52263.47193.69580.0665-0.08810.37110.6362-0.18750.98860.5308-0.39060.07660.3678-0.0121-0.02790.52660.05540.21-37.4168-40.74888.4523
403.93282.11592.14581.6702-0.02633.8062-0.19650.42050.9796-0.2308-0.04380.7043-0.3276-0.64910.27460.3990.00150.02070.55460.04220.2927-35.6227-34.9399.8334
413.00391.9077-0.50922.7497-0.06473.2744-0.0714-0.06230.41440.43110.1560.35570.0312-0.3469-0.0590.39560.02160.03140.49240.03550.1678-34.5936-41.259818.6748
424.09390.1447-2.20560.76180.12681.8508-0.03580.0634-0.3543-0.0274-0.1288-0.03960.2882-0.11540.11380.4001-0.0041-0.01740.38390.0390.1474-23.0642-47.525514.6457
432.95390.9783-1.05342.658-0.08030.3816-0.04720.1792-0.0403-0.08930.0742-0.01440.1014-0.0106-0.01730.36530.0046-0.00030.40130.02030.1132-19.9532-41.51696.0436
442.4499-0.46561.32912.46041.86112.56390.0244-0.3090.1761-0.42880.0454-0.3269-0.01440.2209-0.00730.36850.13170.06930.54190.02190.2183-16.7266-38.896910.6895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )A50 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )A55 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )A60 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )A70 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 88 )A75 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 42 )B17 - 42
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 53 )B43 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 71 )B54 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 79 )B72 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 94 )B80 - 94
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 136 )B95 - 136
12X-RAY DIFFRACTION12chain 'B' and (resid 137 through 145 )B137 - 145
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 169 )B146 - 169
14X-RAY DIFFRACTION14chain 'C' and (resid 50 through 54 )C50 - 54
15X-RAY DIFFRACTION15chain 'C' and (resid 55 through 74 )C55 - 74
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 87 )C75 - 87
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 27 )D18 - 27
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 42 )D28 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 53 )D43 - 53
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 71 )D54 - 71
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 79 )D72 - 79
22X-RAY DIFFRACTION22chain 'D' and (resid 80 through 94 )D80 - 94
23X-RAY DIFFRACTION23chain 'D' and (resid 95 through 118 )D95 - 118
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 169 )D119 - 169
25X-RAY DIFFRACTION25chain 'E' and (resid 51 through 55 )E51 - 55
26X-RAY DIFFRACTION26chain 'E' and (resid 56 through 60 )E56 - 60
27X-RAY DIFFRACTION27chain 'E' and (resid 61 through 70 )E61 - 70
28X-RAY DIFFRACTION28chain 'E' and (resid 71 through 75 )E71 - 75
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 83 )E76 - 83
30X-RAY DIFFRACTION30chain 'E' and (resid 84 through 89 )E84 - 89
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 26 )F14 - 26
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 42 )F27 - 42
33X-RAY DIFFRACTION33chain 'F' and (resid 43 through 94 )F43 - 94
34X-RAY DIFFRACTION34chain 'F' and (resid 95 through 171 )F95 - 171
35X-RAY DIFFRACTION35chain 'G' and (resid 50 through 59 )G50 - 59
36X-RAY DIFFRACTION36chain 'G' and (resid 60 through 69 )G60 - 69
37X-RAY DIFFRACTION37chain 'G' and (resid 70 through 74 )G70 - 74
38X-RAY DIFFRACTION38chain 'G' and (resid 75 through 88 )G75 - 88
39X-RAY DIFFRACTION39chain 'H' and (resid 18 through 28 )H18 - 28
40X-RAY DIFFRACTION40chain 'H' and (resid 29 through 42 )H29 - 42
41X-RAY DIFFRACTION41chain 'H' and (resid 43 through 71 )H43 - 71
42X-RAY DIFFRACTION42chain 'H' and (resid 72 through 94 )H72 - 94
43X-RAY DIFFRACTION43chain 'H' and (resid 95 through 155 )H95 - 155
44X-RAY DIFFRACTION44chain 'H' and (resid 156 through 170 )H156 - 170

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