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- PDB-1uzg: CRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1uzg
TitleCRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN
ComponentsMAJOR ENVELOPE PROTEIN E
KeywordsVIRAL PROTEIN / MEMBRANE FUSION / FLAVIVIRUS / FUSION LOOP / CLASS 2 FUSION PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesDENGUE VIRUS TYPE 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsModis, Y. / Harrison, S.C.
Citation
Journal: J.Virol. / Year: 2005
Title: Variable Surface Epitopes in the Crystal Structure of Dengue Virus Type 3 Envelope Glycoprotein
Authors: Modis, Y. / Ogata, S. / Clements, D. / Harrison, S.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein
Authors: Modis, Y. / Ogata, S. / Clements, D. / Harrison, S.C.
History
DepositionMar 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR ENVELOPE PROTEIN E
B: MAJOR ENVELOPE PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7196
Polymers86,3412
Non-polymers2,3784
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint33.9 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.855, 68.631, 270.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETTHRTHRAA1 - 511 - 51
211METMETTHRTHRBB1 - 511 - 51
121HISHISASPASPAA132 - 190132 - 190
221HISHISASPASPBB132 - 190132 - 190
131PHEPHELYSLYSAA277 - 293277 - 293
231PHEPHELYSLYSBB277 - 293277 - 293
112GLNGLNGLNGLNAA52 - 13152 - 131
212GLNGLNGLNGLNBB52 - 13152 - 131
122PHEPHEILEILEAA191 - 276191 - 276
222PHEPHEILEILEBB191 - 276191 - 276

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.90052, -0.43253, 0.04449), (-0.43332, 0.88423, -0.17428), (0.03604, -0.17622, -0.98369)
Vector: 20.99702, 7.05981, 29.74221)
DetailsTHE VIRION OF THIS VIRUS IS A NUCLEOCAPSID COVERED BY ALIPOPROTEIN ENVELOPE CONSISTING OF A LIPID MEMBRANE AND 2ENVELOPE GLYCOPROTEINS, M AND E. THE NUCLEOCAPSID IS ACOMPLEX OF PROTEIN C AND MRNA.

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Components

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Protein / Non-polymers , 2 types, 16 molecules AB

#1: Protein MAJOR ENVELOPE PROTEIN E / DENGUE VIRUS TYPE 2 MAJOR ENVELOPE PROTEIN E


Mass: 43170.398 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS TYPE 3 / Cell line: DROSOPHILA SCHNEIDER 2 / Plasmid: PMTT / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P27915
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 4 molecules

#2: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-2-2-3/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Compound detailsCATALYTIC ACTIVITY: SELECTIVE HYDROLYSIS OF XAA-XAA-|-XBB BONDS IN WHICH EACH OF THE XAA CAN BE ...CATALYTIC ACTIVITY: SELECTIVE HYDROLYSIS OF XAA-XAA-|-XBB BONDS IN WHICH EACH OF THE XAA CAN BE EITHER ARG OR LYS AND XBB CAN BE EITHER SER OR ALA. CATALYTIC ACTIVITY: N NUCLEOSIDE TRIPHOSPHATE = N DIPHOSPHATE + {RNA}(N).
Sequence detailsRESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION LOOP (ALLISON ET AL., J.VIROL. 75, 4268- ...RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION LOOP (ALLISON ET AL., J.VIROL. 75, 4268-75 (2001)) RESIDUES 268-277 FORM THE KL-HAIRPIN, WHICH MEDIATES THE FUSION-ACTIVATING CONFORMATIONAL CHANGE. THE KL HAIRPIN IS IN THE CLOSED CONFORMATION.

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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: 2.737 Å3/Da / Density % sol: 55.1 %
Crystal growpH: 8.5 / Details: 15% PEG 8K, 0.2 M LICL2, 0.1 M TRIS/HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2003 / Details: RH-COATED SI MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.6→21 Å / Num. obs: 12090 / % possible obs: 91.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.3
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.6 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SOLVEphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAN

1oan


Resolution: 3.5→20.99 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.867 / SU B: 52.79 / SU ML: 0.827 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.862 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.324 603 5.1 %RANDOM
Rwork0.284 ---
obs0.286 11159 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--2 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 158 14 6214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9838590
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8855782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.22658
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6471.53874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.91626262
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.45532460
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0844.52328
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 39
Rwork0.349 646
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)
14.6822-0.97-2.8181.5246-1.12053.0919-0.059-0.0483-0.25430.4924-0.1678-0.0244-0.38670.42570.22680.4738-0.10820.05690.0601-0.07580.118411.067-0.05158.847
20.21620.8261-1.35460.3692-1.43749.4142-0.11380.14060.0411-0.0630.0417-0.0883-0.31390.15540.07210.2381-0.10490.07330.2587-0.05410.355225.7721.11612.414
33.02090.47151.41132.47332.62056.2670.1721-0.1859-0.41920.19960.06890.2427-0.1914-0.2799-0.2410.54830.09220.23590.16190.13250.2295-11.383-0.78371.172
45.8291.9401-2.31962.36280.09142.38210.00910.0158-0.20130.355-0.37350.07220.0117-0.41750.36450.3267-0.02810.06440.2891-0.24240.312513.572-7.983-27.695
51.7037-0.7094-2.98871.09411.1466.93540.00890.2863-0.1709-0.10710.16510.0974-0.03890.0764-0.17390.2347-0.04540.11740.2769-0.10380.3294-2.101-5.3418.215
63.40221.782-2.39345.5433-2.589910.4176-0.0653-0.3191-0.5023-0.3717-0.0976-0.4187-0.0310.21030.1630.30670.02450.040.1466-0.09320.252734.777-1.08-40.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 51
2X-RAY DIFFRACTION1A132 - 190
3X-RAY DIFFRACTION1A277 - 293
4X-RAY DIFFRACTION2A52 - 131
5X-RAY DIFFRACTION2A191 - 276
6X-RAY DIFFRACTION3A294 - 392
7X-RAY DIFFRACTION4B1 - 51
8X-RAY DIFFRACTION4B132 - 190
9X-RAY DIFFRACTION4B277 - 293
10X-RAY DIFFRACTION5B52 - 131
11X-RAY DIFFRACTION5B191 - 276
12X-RAY DIFFRACTION6B294 - 392

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