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- PDB-5ot2: RNA polymerase II elongation complex in the presence of 3d-Napht-A -

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Basic information

Entry
Database: PDB / ID: 5ot2
TitleRNA polymerase II elongation complex in the presence of 3d-Napht-A
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA non-template strand
  • DNA template strand
  • RNA product strand
KeywordsTRANSCRIPTION / Inhibitor / Complex / Polymerase
Function / homology
Function and homology information


RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / Growth Hormone; Chain: A; / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / Gyrase A; domain 2 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / S1 domain / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
Similarity search - Domain/homology
2-ethyl-7-methoxy-naphthalene / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...2-ethyl-7-methoxy-naphthalene / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMalvezzi, S. / Farnung, L. / Aloisi, C. / Angelov, T. / Cramer, P. / Sturla, S.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Mechanism of RNA polymerase II stalling by DNA alkylation.
Authors: Malvezzi, S. / Farnung, L. / Aloisi, C.M.N. / Angelov, T. / Cramer, P. / Sturla, S.J.
History
DepositionAug 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.0Jul 30, 2025Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
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_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
T: DNA template strand
N: DNA non-template strand
P: RNA product strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,69625
Polymers529,96215
Non-polymers73410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71290 Å2
ΔGint-357 kcal/mol
Surface area155590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.350, 394.930, 283.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P34087
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P27999
#11: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20434
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20436
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22139
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

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DNA chain , 2 types, 2 molecules TN

#13: DNA chain DNA template strand


Mass: 7841.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain DNA non-template strand


Mass: 4359.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules P

#15: RNA chain RNA product strand


Mass: 3602.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 10 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / References: DNA-directed RNA polymerase
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / References: DNA-directed RNA polymerase
#18: Chemical ChemComp-AHW / 2-ethyl-7-methoxy-naphthalene


Mass: 186.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14O

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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: 5.85 Å3/Da / Density % sol: 78.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4-7% PEG 6000, 200 mM ammonium acetate, 300 mM sodium acetate, 50 mM HEPES pH 7.0, 5 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.2→49.882 Å / Num. obs: 202994 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 16.38
Reflection shellResolution: 3.2→3.31 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.882 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2218 3272 0.83 %
Rwork0.1785 --
obs0.1789 202994 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30950 761 3 0 31714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732432
X-RAY DIFFRACTIONf_angle_d1.03343837
X-RAY DIFFRACTIONf_dihedral_angle_d6.2419680
X-RAY DIFFRACTIONf_chiral_restr0.0584934
X-RAY DIFFRACTIONf_plane_restr0.0075552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24770.32881440.321417083X-RAY DIFFRACTION100
3.2477-3.29850.31391260.317917143X-RAY DIFFRACTION100
3.2985-3.35260.3991450.330617006X-RAY DIFFRACTION100
3.3526-3.41040.38141480.313717020X-RAY DIFFRACTION100
3.4104-3.47240.33161450.287417116X-RAY DIFFRACTION100
3.4724-3.53910.28171450.257117113X-RAY DIFFRACTION100
3.5391-3.61130.26571380.242616987X-RAY DIFFRACTION100
3.6113-3.68980.2491400.22917091X-RAY DIFFRACTION100
3.6898-3.77560.28031500.224117115X-RAY DIFFRACTION100
3.7756-3.870.25341420.203117055X-RAY DIFFRACTION100
3.87-3.97460.23161490.188417023X-RAY DIFFRACTION100
3.9746-4.09150.24231450.172917100X-RAY DIFFRACTION100
4.0915-4.22350.23171360.163217044X-RAY DIFFRACTION100
4.2235-4.37440.22621380.151817116X-RAY DIFFRACTION100
4.3744-4.54940.17291440.141317070X-RAY DIFFRACTION100
4.5494-4.75630.20161500.135517061X-RAY DIFFRACTION100
4.7563-5.00690.22431380.141217110X-RAY DIFFRACTION100
5.0069-5.32020.17991420.149717063X-RAY DIFFRACTION100
5.3202-5.73050.20281410.166117083X-RAY DIFFRACTION100
5.7305-6.30610.21261450.178917135X-RAY DIFFRACTION100
6.3061-7.21630.25991500.182417047X-RAY DIFFRACTION100
7.2163-9.08280.18151270.157817117X-RAY DIFFRACTION100
9.0828-49.88780.18011440.167717022X-RAY DIFFRACTION100
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)
10.692-0.1235-0.04320.78960.00741.06390.0206-0.1453-0.3477-0.146-0.09960.04690.1451-0.057-00.93910.0026-0.07960.97820.11261.0293-2.6027-49.65218.3981
20.78090.2747-0.16180.35480.01350.1777-0.03830.146-0.6752-0.1197-0.0636-0.12750.1575-0.01180.00011.09450.0007-0.0891.13890.06951.61912.6974-77.74545.2702
30.61681.3824-0.24192.5702-0.00540.8490.08710.42010.03880.36590.01361.48650.3281-0.4906-0.00091.2615-0.0386-0.2371.3540.14532.2016-49.0166-43.2795-10.8663
40.82250.4830.15240.9131-0.27060.0723-0.0230.2368-0.1917-0.04410.16430.51590.0686-0.22070.00061.2867-0.0685-0.27361.35330.04831.7678-37.9832-50.5656-9.0584
51.33220.60590.392.0544-0.82512.4425-0.0182-0.14410.03920.49130.29920.1415-0.2460.03220.00091.2507-0.1678-0.0681.2435-0.1131.9143-45.7925-85.11717.1143
60.42250.5909-0.17041.3886-0.0529-0.0634-0.00540.0161-0.40190.22840.01420.54610.2244-0.05470.0021.3757-0.1045-0.19191.1910.06551.438-36.6745-57.0825-2.0636
70.9937-0.1326-0.48932.23870.05271.9601-0.18640.3605-0.3894-0.64460.10410.60070.1622-0.26180.00321.5617-0.2526-0.61191.4098-0.1091.7408-41.7122-68.4661-26.5609
81.1716-0.4283-0.24032.5785-0.28970.8477-0.1994-0.0556-0.1338-0.03160.15840.574-0.045-0.1584-0.00061.1090.0444-0.2211.05730.0120.8646-17.5607-30.8299-14.9891
90.6292-0.00760.09250.4166-0.08972.2767-0.0321-0.098-0.1272-0.2006-0.00870.0514-0.1031-0.11660.00020.9217-0.0229-0.06941.0540.06320.8671-1.6862-37.6519.2415
100.1185-0.0405-0.07460.2689-0.0740.07990.20190.2417-0.0181-0.4304-0.0220.1006-0.4004-0.07320.00071.75580.12060.0891.3950.08460.88889.4035-18.7876-50.0724
110.44370.40180.04060.36190.17150.2025-0.4958-0.2272-0.1289-0.11120.23790.32450.09110.5692-0.00011.42060.0031-0.07711.15340.22370.61282.1198-14.8509-31.487
121.30820.5718-0.67932.30920.061.27160.00890.34640.4067-0.49260.03110.3575-0.10390.00950.00021.49730.0574-0.31581.06120.11821.0404-15.7326-6.3614-29.5035
130.7363-0.32330.04040.12440.12720.1892-0.18230.4079-0.2095-0.36290.0782-0.17980.19150.2681-0.00051.7956-0.04820.01181.377-0.02680.90546.4507-34.5252-42.9461
140.9356-0.5138-0.00750.58580.32380.08110.04290.51280.035-0.6154-0.1017-0.405-0.14640.143-0.00081.72580.03910.02711.36080.21171.015914.6825-19.7937-40.4005
150.0562-0.00170.07160.04330.08970.1636-0.3259-1.1656-0.05160.1905-0.01930.67-0.2203-0.6968-0.00081.2282-0.1224-0.00851.940.03721.2358.1155-41.248253.3899
161.2393-0.449-0.34170.5265-0.7521.8766-0.19460.3003-0.0087-0.5830.18-0.2726-0.20860.87260.00021.2607-0.26480.00461.7226-0.10411.125828.2086-26.788558.5347
171.2365-0.4111-0.38760.99440.61771.185-0.2522-0.34660.2397-0.47020.2424-0.3161-0.17350.81820.00081.208-0.1077-0.08811.6764-0.10621.063624.9515-29.031272.1706
180.0612-0.0606-0.10680.14920.19550.2557-0.1452-0.5453-0.37140.31820.0536-0.5835-0.45420.75370.00121.2388-0.1469-0.0161.8284-0.21041.07131.3265-30.550882.8501
190.64960.06660.28510.15210.47941.13240.1869-0.0404-0.86850.6303-0.1628-0.35250.72240.16340.00241.71970.0341-0.10351.28730.34152.558517.0248-103.136623.356
200.0918-0.1259-0.14470.15520.21670.28-0.1492-0.92120.07910.84250.24850.5332-0.09710.1104-0.00261.8649-0.06830.19431.75510.62752.24477.6822-99.032337.2778
210.4069-0.02290.51421.75180.55820.79370.1963-0.4957-0.72890.3625-0.1294-0.20810.4693-0.13780.00041.1725-0.0166-0.14741.14750.38571.600517.0216-78.972224.029
220.05550.07140.06350.10260.08760.075-0.1712-0.97310.54480.7974-0.1342-0.7738-0.81050.1784-0.00391.1498-0.029-0.30061.35750.15451.304729.6176-51.247435.1544
230.07330.0459-0.02830.1028-0.0350.1402-0.2117-0.457-0.9482-0.2188-0.0582-0.16260.70961.20990.00281.01550.0215-0.07171.10980.14771.006930.9319-49.80419.2988
240.10680.0679-0.15630.0708-0.06720.22090.0360.2577-0.3769-0.55850.01550.728-0.2247-0.1889-0.00030.8660.0088-0.12331.01650.10840.724422.3936-35.593816.8728
250.0786-0.0420.0890.1483-0.06330.1090.4158-0.01610.32-0.14920.008-0.6359-0.55420.38240.00061.6044-0.0732-0.0251.26330.1741.114229.0032-23.303514.9977
260.07650.0253-0.00370.04330.00810.02160.17780.0062-0.1278-0.9564-0.0996-0.5790.1287-0.0980.00051.1158-0.11820.07451.29030.19170.929128.559-30.227511.6836
270.0444-0.008-0.02750.0163-0.01160.05960.29270.82760.0869-0.1232-0.1936-0.18030.56080.70740.00010.8495-0.0597-0.05941.04280.05841.248233.2589-33.606519.3102
280.0830.0383-0.01960.0244-0.02670.03080.047-0.2655-0.03531.03070.1213-0.4802-0.1333-0.6441-0.00080.9220.0281-0.08981.18690.2721.063323.2572-49.073528.1399
290.0137-0.0052-0.0080.03470.04830.05640.4364-0.1178-0.1031-0.3895-0.45590.1842-0.52270.0978-0.00211.0354-0.2302-0.04631.4373-0.02010.815329.2644-46.820227.2434
300.1217-0.0305-0.01260.0771-0.05910.0610.46371.3981-0.136-0.9289-0.30760.05360.25810.22080.00210.8964-0.0023-0.10561.30320.05461.255433.3019-43.146115.7115
31-0.02260.01780.00850.03050.05330.06490.2755-0.14450.3642-0.64370.4419-0.0960.3387-0.25460.0060.9659-0.1506-0.00821.5411-0.13440.91920.6683-31.651650.5348
320.00980.01460.03130.03620.07440.11950.0515-0.01740.5327-0.24390.4370.61-1.30380.19250.00091.4432-0.3364-0.06151.5732-0.02051.118225.272-23.639936.3624
330.02880.05990.1504-0.01410.14340.42490.0671-0.4690.1748-0.07540.1651-0.19110.0390.8029-0.00051.1567-0.2184-0.07041.59980.01031.107621.9891-30.588844.7807
340.76610.0715-0.11520.6562-0.09480.43160.0828-0.25840.35760.4213-0.22920.6746-0.4156-0.2301-0.0011.2687-0.0623-0.031.455-0.08221.15128.787-16.549275.4712
350.5312-0.5093-0.32430.47550.32630.19690.1632-0.25590.2658-0.17420.07670.1821-0.0970.5716-0.0031.2469-0.1072-0.01351.3902-0.00551.09739.173-23.357372.5702
360.1219-0.09430.19840.254-0.03290.2733-0.50470.5798-0.6789-0.51270.3165-0.45980.80870.22740.00111.89550.33880.49211.8002-0.17711.41237.7643-57.5833-40.1985
370.48510.15-0.14730.3048-0.2140.13140.42620.3940.0037-1.1379-0.4166-0.1407-0.4698-0.084-0.00111.60510.12610.47141.7101-0.01971.155439.5449-45.0777-38.8674
388.12791.64456.66264.45743.07486.1928-0.87540.82621.1047-0.2550.09220.4856-0.5079-0.0557-2.85741.1813-0.62370.67031.6250.66631.5343.7647-31.7088-39.7197
390.69540.32710.37610.23680.16490.2087-0.72840.720.86480.0056-0.25830.7133-0.1540.6138-0.0881.76110.32170.59271.87030.23331.700940.237-45.7935-37.2515
400.0482-0.0397-0.04680.1510.02530.05090.4368-0.0018-0.52850.29440.4638-0.5657-0.19240.12560.00021.78870.44780.20081.54410.03391.831144.9695-64.8504-25.9248
410.0862-0.08390.00760.0639-0.0060.029-0.120.408-1.3586-0.62380.1231-0.7718-0.05890.7489-0.00311.91680.42180.37611.40050.16431.702939.8132-57.9173-30.8331
420.03320.03510.01450.072-0.04770.1336-0.1289-0.4138-0.3044-0.0267-0.8153-0.1756-0.5910.1092-0.00492.15950.69050.21592.1903-0.0042.124349.8554-54.4178-28.9391
430.0357-0.00980.06120.0936-0.01480.0813-0.4240.50770.0854-0.2730.1089-0.5418-0.34290.1336-0.00381.76270.3210.45072.26070.39741.153442.8656-47.5925-41.8556
440.8549-0.516-0.49440.27020.2220.19550.1098-0.6428-0.0221-0.0603-0.1334-0.49270.12160.289-0.00021.2676-0.2811-0.06631.3732-0.02532.1692-42.138-109.39752.0376
450.7273-0.36590.12130.115-0.02460.0595-0.56660.3624-0.3006-0.8402-0.2560.96890.7088-0.1727-0.0012.2324-0.2855-0.41231.4304-0.23181.9928-29.3793-91.2974-27.2038
460.0781-0.07080.11540.0426-0.10470.1495-0.60620.31210.4977-0.8346-0.30880.3468-0.1662-0.4519-0.00571.49670.0973-0.30490.92060.15560.7881-13.8717-22.1831-34.3165
470.0584-0.0297-0.04970.0495-0.01250.0587-0.01320.9418-0.1083-0.03910.62910.43330.4386-0.43480.0021.6280.1632-0.5261.77250.00381.2176-25.8014-26.8797-45.4863
480.04030.05610.08440.19710.11120.1194-0.02210.7639-0.1295-0.46370.16920.50080.30140.03630.00051.66530.079-0.20361.28810.03070.8073-15.0442-29.551-40.6397
490.09510.0025-0.01280.05710.00370.0434-0.40750.01160.03050.2855-0.14660.1479-0.4312-0.7848-0.00171.4047-0.0132-0.32961.36940.15741.041-33.607-22.9394-25.7636
500.08410.0968-0.1110.111-0.13770.10230.0847-0.09740.6372-0.2192-0.0133-0.4776-0.76630.5884-0.00251.45170.0203-0.02341.230.15241.16266.8521-13.6116-15.3179
510.1133-0.1949-0.19420.31960.29850.3065-0.12750.8486-0.2859-0.0126-0.2741-0.53190.09110.4492-0.00141.26450.03410.10871.2060.08821.163926.2471-18.5752-18.9724
520.0588-0.04410.00970.0363-0.02450.055-0.14621.1575-0.8858-0.9009-0.031-0.23160.1060.0729-0.00281.40630.0640.22141.2650.18660.824925.3994-22.7018-30.9773
530.1034-0.11120.1070.1249-0.16550.1744-0.0679-0.52050.6932-0.3875-0.075-0.5074-0.34510.45220.00151.1323-0.08760.12121.30160.23671.167924.2132-21.6969-21.6672
540.1595-0.16750.00080.31710.18080.2768-0.06990.95480.5058-1.0590.0161-0.6637-0.33190.38840.01651.7262-0.15880.06161.570.35720.859319.8817-11.762-40.5628
550.09120.01730.04620.00110.00650.0194-0.37370.4152-0.1998-0.0532-0.6668-0.0142-0.1562-0.07540.0032.3036-0.01590.05852.03880.17870.83862.5543-10.9965-56.6862
560.02690.0023-0.0440.0465-0.06770.16150.1622-0.4085-0.05580.32780.41420.07570.4263-0.6462-0.00021.2966-0.05020.02621.19910.28921.3419-37.6071-8.1452-8.4759
570.2234-0.133-0.3760.07850.22220.6312-0.20860.27380.22790.01230.2389-0.196-0.11280.38450.34210.7424-0.0768-0.82430.90370.41582.1193-43.1461-13.9518-14.5826
580.0629-0.05210.02250.0534-0.01950.00470.1429-0.08230.61450.3581-0.87150.1773-0.6838-0.6199-0.01211.67480.26270.28181.53480.00651.9767-42.0875-7.1322-1.8859
591.4316-0.3659-0.6740.09330.17190.31810.49450.3350.1758-0.5266-0.18580.09270.0291-0.05880.30041.92030.8266-1.03521.1853-0.64972.9112-48.6787-11.5882-10.1593
600.06220.0557-0.010.05690.00280.08960.5204-0.1467-0.2259-0.7581-0.30291.1964-0.4918-0.30560.00591.32320.1681-0.28811.44980.24072.422-41.1479-15.9796-7.4337
610.03910.02070.02120.136-0.06680.07930.707-0.64620.7280.05880.36540.111-0.38240.37380.00311.62560.0556-0.1221.26060.10871.1795-18.7558-7.6883-14.3168
621.8740.62790.44231.08420.32211.3725-0.07670.13910.0407-0.52280.13570.0749-0.8059-0.6728-0.00082.8058-0.54440.5652.5463-0.36253.8137-20.8586-74.114122.2169
630.3920.3362-0.25340.3519-0.54110.8921-0.33320.0439-0.62320.31040.79420.93710.4414-0.2532-0.00031.41430.1298-0.02461.7190.08331.7385-17.3659-43.77637.0563
640.3038-0.09690.2920.14760.09130.5516-0.03880.108-0.4982-0.6324-1.4070.8805-0.8812-0.93170.05293.314-0.06510.21222.8698-0.64533.6155-14.5768-69.817314.5116
650.03490.0062-0.05040.0043-0.00670.07480.08370.1616-0.0113-0.28480.162-0.01650.0793-0.05430.01335.13031.3165-0.38374.0524-0.23522.7348-15.2221-73.48327.7678
660.10270.0745-0.21570.1725-0.08880.2345-0.3961-0.8793-0.51150.85970.50930.5630.8605-0.2526-0.00451.59430.1741-0.14471.80270.0941.3273-19.5944-40.11594.829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 845 )
2X-RAY DIFFRACTION2chain 'A' and (resid 846 through 1454 )
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 171 )
4X-RAY DIFFRACTION4chain 'B' and (resid 172 through 242 )
5X-RAY DIFFRACTION5chain 'B' and (resid 243 through 370 )
6X-RAY DIFFRACTION6chain 'B' and (resid 371 through 538 )
7X-RAY DIFFRACTION7chain 'B' and (resid 539 through 744 )
8X-RAY DIFFRACTION8chain 'B' and (resid 745 through 1051 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1052 through 1224 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 26 )
11X-RAY DIFFRACTION11chain 'C' and (resid 27 through 51 )
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 163 )
13X-RAY DIFFRACTION13chain 'C' and (resid 164 through 209 )
14X-RAY DIFFRACTION14chain 'C' and (resid 210 through 267 )
15X-RAY DIFFRACTION15chain 'D' and (resid 3 through 23 )
16X-RAY DIFFRACTION16chain 'D' and (resid 24 through 133 )
17X-RAY DIFFRACTION17chain 'D' and (resid 134 through 203 )
18X-RAY DIFFRACTION18chain 'D' and (resid 204 through 221 )
19X-RAY DIFFRACTION19chain 'E' and (resid 4 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 130 )
21X-RAY DIFFRACTION21chain 'E' and (resid 131 through 215 )
22X-RAY DIFFRACTION22chain 'F' and (resid 69 through 78 )
23X-RAY DIFFRACTION23chain 'F' and (resid 79 through 86 )
24X-RAY DIFFRACTION24chain 'F' and (resid 87 through 102 )
25X-RAY DIFFRACTION25chain 'F' and (resid 103 through 116 )
26X-RAY DIFFRACTION26chain 'F' and (resid 117 through 126 )
27X-RAY DIFFRACTION27chain 'F' and (resid 127 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 142 )
29X-RAY DIFFRACTION29chain 'F' and (resid 143 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 155 )
31X-RAY DIFFRACTION31chain 'G' and (resid 1 through 13 )
32X-RAY DIFFRACTION32chain 'G' and (resid 14 through 34 )
33X-RAY DIFFRACTION33chain 'G' and (resid 35 through 79 )
34X-RAY DIFFRACTION34chain 'G' and (resid 80 through 151 )
35X-RAY DIFFRACTION35chain 'G' and (resid 152 through 171 )
36X-RAY DIFFRACTION36chain 'H' and (resid 2 through 43 )
37X-RAY DIFFRACTION37chain 'H' and (resid 44 through 81 )
38X-RAY DIFFRACTION38chain 'H' and (resid 82 through 91 )
39X-RAY DIFFRACTION39chain 'H' and (resid 92 through 101 )
40X-RAY DIFFRACTION40chain 'H' and (resid 102 through 110 )
41X-RAY DIFFRACTION41chain 'H' and (resid 111 through 127 )
42X-RAY DIFFRACTION42chain 'H' and (resid 128 through 140 )
43X-RAY DIFFRACTION43chain 'H' and (resid 141 through 146 )
44X-RAY DIFFRACTION44chain 'I' and (resid 2 through 52 )
45X-RAY DIFFRACTION45chain 'I' and (resid 53 through 115 )
46X-RAY DIFFRACTION46chain 'J' and (resid 1 through 17 )
47X-RAY DIFFRACTION47chain 'J' and (resid 18 through 31 )
48X-RAY DIFFRACTION48chain 'J' and (resid 32 through 55 )
49X-RAY DIFFRACTION49chain 'J' and (resid 56 through 65 )
50X-RAY DIFFRACTION50chain 'K' and (resid 1 through 18 )
51X-RAY DIFFRACTION51chain 'K' and (resid 19 through 39 )
52X-RAY DIFFRACTION52chain 'K' and (resid 40 through 62 )
53X-RAY DIFFRACTION53chain 'K' and (resid 63 through 82 )
54X-RAY DIFFRACTION54chain 'K' and (resid 83 through 109 )
55X-RAY DIFFRACTION55chain 'K' and (resid 110 through 114 )
56X-RAY DIFFRACTION56chain 'L' and (resid 27 through 31 )
57X-RAY DIFFRACTION57chain 'L' and (resid 32 through 36 )
58X-RAY DIFFRACTION58chain 'L' and (resid 37 through 46 )
59X-RAY DIFFRACTION59chain 'L' and (resid 47 through 51 )
60X-RAY DIFFRACTION60chain 'L' and (resid 52 through 58 )
61X-RAY DIFFRACTION61chain 'L' and (resid 59 through 70 )
62X-RAY DIFFRACTION62chain 'T' and (resid 10 through 14 )
63X-RAY DIFFRACTION63chain 'T' and (resid 15 through 28 )
64X-RAY DIFFRACTION64chain 'N' and (resid 1 through 5 )
65X-RAY DIFFRACTION65chain 'N' and (resid 6 through 7 )
66X-RAY DIFFRACTION66chain 'P' and (resid 1 through 10 )

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