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- PDB-5m8s: Crystal structure of human tyrosinase related protein 1 mutant (T... -

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Basic information

Entry
Database: PDB / ID: 5m8s
TitleCrystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in complex with phenylthiourea (PTU)
Components5,6-dihydroxyindole-2-carboxylic acid oxidase
KeywordsUNKNOWN FUNCTION / human tyrosinase related protein 1 / melanin biosynthesis / tyrosinase / OXIDOREDUCTASE
Function / homology
Function and homology information


acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome membrane / melanosome organization / intracellular vesicle ...acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome membrane / melanosome organization / intracellular vesicle / Regulation of MITF-M-dependent genes involved in pigmentation / clathrin-coated endocytic vesicle membrane / melanosome / oxidoreductase activity / endosome membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
N-PHENYLTHIOUREA / 5,6-dihydroxyindole-2-carboxylic acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLai, X. / Soler-Lopez, M. / Wichers, H.J. / Dijkstra, B.W.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Phenylthiourea Binding to Human Tyrosinase-Related Protein 1
Authors: Lai, X. / Wichers, H.J. / Soler-Lopez, M. / Dijkstra, B.W.
History
DepositionOct 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 1.2Feb 12, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5,6-dihydroxyindole-2-carboxylic acid oxidase
B: 5,6-dihydroxyindole-2-carboxylic acid oxidase
C: 5,6-dihydroxyindole-2-carboxylic acid oxidase
D: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,92737
Polymers202,1254
Non-polymers10,80333
Water13,007722
1
A: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5209
Polymers50,5311
Non-polymers1,9898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6749
Polymers50,5311
Non-polymers3,1438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,69410
Polymers50,5311
Non-polymers2,1639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0399
Polymers50,5311
Non-polymers3,5088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.081, 141.767, 191.730
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 (resseq 25:33 or resseq 35:36 or resseq...
21(chain B and (resseq 25:33 or resseq 35:36 or resseq...
31(chain C and (resseq 25:33 or resseq 35:36 or resseq...
41(chain D and (resseq 25:33 or resseq 35:36 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 33
121(chain A and (resseq 25:33 or resseq 35:36 or resseq...A35 - 36
131(chain A and (resseq 25:33 or resseq 35:36 or resseq...A38 - 70
141(chain A and (resseq 25:33 or resseq 35:36 or resseq...A71
151(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
161(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
171(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
181(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
191(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
1101(chain A and (resseq 25:33 or resseq 35:36 or resseq...A25 - 3852
211(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 33
221(chain B and (resseq 25:33 or resseq 35:36 or resseq...B35 - 36
231(chain B and (resseq 25:33 or resseq 35:36 or resseq...B38 - 70
241(chain B and (resseq 25:33 or resseq 35:36 or resseq...B71
251(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
261(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
271(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
281(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
291(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
2101(chain B and (resseq 25:33 or resseq 35:36 or resseq...B25 - 3852
311(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 33
321(chain C and (resseq 25:33 or resseq 35:36 or resseq...C35 - 36
331(chain C and (resseq 25:33 or resseq 35:36 or resseq...C38 - 70
341(chain C and (resseq 25:33 or resseq 35:36 or resseq...C71
351(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
361(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
371(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
381(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
391(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
3101(chain C and (resseq 25:33 or resseq 35:36 or resseq...C25 - 3851
411(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 33
421(chain D and (resseq 25:33 or resseq 35:36 or resseq...D35 - 36
431(chain D and (resseq 25:33 or resseq 35:36 or resseq...D38 - 70
441(chain D and (resseq 25:33 or resseq 35:36 or resseq...D71
451(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852
461(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852
471(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852
481(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852
491(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852
4101(chain D and (resseq 25:33 or resseq 35:36 or resseq...D25 - 3852

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
5,6-dihydroxyindole-2-carboxylic acid oxidase / DHICA oxidase / Catalase B / Glycoprotein 75 / Melanoma antigen gp75 / Tyrosinase-related protein 1 / TRP1


Mass: 50531.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYRP1, CAS2, TYRP, TYRRP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P17643, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor

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Sugars , 8 types, 20 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-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
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_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)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-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
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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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Non-polymers , 3 types, 735 molecules

#10: Chemical
ChemComp-URS / N-PHENYLTHIOUREA


Mass: 152.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2S
#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (pH 7.0), 0.2 M NaCl and 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→48.92 Å / Num. obs: 124119 / % possible obs: 99.4 % / Redundancy: 4 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.2data extraction
PHENIX1.10.1_2155refinement
SCALAdata scaling
PHENIXphasing
RefinementResolution: 2.2→45.883 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.2349 6286 5.07 %
Rwork0.1936 --
obs0.1957 124042 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.15 Å2 / Biso mean: 44.2635 Å2 / Biso min: 21.61 Å2
Refinement stepCycle: final / Resolution: 2.2→45.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14216 0 684 722 15622
Biso mean--59.12 45.52 -
Num. residues----1784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8439X-RAY DIFFRACTION7.231TORSIONAL
12B8439X-RAY DIFFRACTION7.231TORSIONAL
13C8439X-RAY DIFFRACTION7.231TORSIONAL
14D8439X-RAY DIFFRACTION7.231TORSIONAL

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