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- PDB-7yob: Crystal structure of Aldehyde dehydrogenase 1A1 from mouse -

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Basic information

Entry
Database: PDB / ID: 7yob
TitleCrystal structure of Aldehyde dehydrogenase 1A1 from mouse
ComponentsAldehyde dehydrogenase 1A1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


fructose catabolic process / 9-cis-retinoic acid metabolic process / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / optic cup morphogenesis involved in camera-type eye development / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity ...fructose catabolic process / 9-cis-retinoic acid metabolic process / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / optic cup morphogenesis involved in camera-type eye development / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / retinoic acid biosynthetic process / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / embryonic eye morphogenesis / aminobutyraldehyde dehydrogenase activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / negative regulation of cold-induced thermogenesis / retinal dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / NAD binding / response to ethanol / response to oxidative stress / response to xenobiotic stimulus / positive regulation of apoptotic process / axon / synapse / apoptotic process / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsZhang, X.Y. / Ouyang, Z.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870751 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of aldehyde dehydrogenase 1A1 from mouse.
Authors: Zhang, X. / Ouyang, Z.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 2.0Aug 31, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity_poly / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ncs_ens_gen / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
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_seq_id / _atom_site.occupancy / _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_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.angle_beta / _cell.volume / _entity_poly.pdbx_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_ncs_dom.details / _struct_ncs_dom.id / _struct_ncs_dom.pdbx_ens_id / _struct_ncs_ens.id / _struct_ncs_ens_gen.dom_id_1 / _struct_ncs_ens_gen.dom_id_2 / _struct_ncs_ens_gen.ens_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id / _symmetry.space_group_name_Hall
Description: Model orientation/position / Details: replace the unplausible assembly of chain F / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1
E: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1


Theoretical massNumber of molelcules
Total (without water)442,9088
Polymers442,9088
Non-polymers00
Water0
1
A: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1


Theoretical massNumber of molelcules
Total (without water)221,4544
Polymers221,4544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1


Theoretical massNumber of molelcules
Total (without water)221,4544
Polymers221,4544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.062, 156.484, 129.209
Angle α, β, γ (deg.)90.000, 97.970, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 16 or (resid 17...
21(chain B and (resid 10 through 14 or (resid 15...
31(chain C and (resid 10 through 14 or (resid 15...
41(chain D and (resid 10 through 14 or (resid 15...
51(chain E and (resid 10 through 14 or (resid 15...
61(chain F and (resid 10 through 14 or (resid 15...
71(chain G and (resid 10 through 14 or (resid 15...
81(chain H and (resid 10 through 14 or (resid 15...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain A and (resid 10 through 16 or (resid 17...AA10 - 1616 - 22
12LYSLYSLYSLYS(chain A and (resid 10 through 16 or (resid 17...AA1723
13ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
14ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
15ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
16ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
21PROPROALAALA(chain B and (resid 10 through 14 or (resid 15...BB10 - 1416 - 20
22ASPASPASPASP(chain B and (resid 10 through 14 or (resid 15...BB1521
23ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
24ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
25ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
26ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
31PROPROALAALA(chain C and (resid 10 through 14 or (resid 15...CC10 - 1416 - 20
32ASPASPASPASP(chain C and (resid 10 through 14 or (resid 15...CC1521
33ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
34ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
35ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
36ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
41PROPROALAALA(chain D and (resid 10 through 14 or (resid 15...DD10 - 1416 - 20
42ASPASPASPASP(chain D and (resid 10 through 14 or (resid 15...DD1521
43ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
44ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
45ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
46ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
51PROPROALAALA(chain E and (resid 10 through 14 or (resid 15...EE10 - 1416 - 20
52ASPASPASPASP(chain E and (resid 10 through 14 or (resid 15...EE1521
53ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
54ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
55ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
56ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
61PROPROALAALA(chain F and (resid 10 through 14 or (resid 15...FH10 - 1416 - 20
62ASPASPASPASP(chain F and (resid 10 through 14 or (resid 15...FH1521
63ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
64ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
65ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
66ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
71PROPROALAALA(chain G and (resid 10 through 14 or (resid 15...GF10 - 1416 - 20
72ASPASPASPASP(chain G and (resid 10 through 14 or (resid 15...GF1521
73PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
74PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
75PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
76PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
81PROPROALAALA(chain H and (resid 10 through 14 or (resid 15...HG10 - 1416 - 20
82ASPASPASPASP(chain H and (resid 10 through 14 or (resid 15...HG1521
83ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
84ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
85ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
86ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507

NCS oper:
IDCodeMatrixVector
1given(-0.994622739484, 0.025589826097, -0.100353210719), (0.0234065290723, -0.888375363262, -0.458520826514), (-0.10088478824, -0.458404160922, 0.882999368489)115.61854429, 39.194571808, 15.8121837614
2given(0.606864027517, 0.751352854253, 0.259200579689), (0.751118296926, -0.64878451268, 0.122065392838), (0.259879503094, 0.12061320206, -0.958078858633)7.54528164651, -4.42927831632, -33.8949320895
3given(-0.602561526163, -0.781726076994, -0.160698312797), (-0.779813904464, 0.533891463151, 0.326879457873), (-0.169734738908, 0.32227976375, -0.931303319163)110.973270072, 59.2781337869, -13.2166546
4given(0.652849206752, -0.560368099466, -0.509681769679), (-0.682430515341, -0.143083745199, -0.716809342567), (0.328749912508, 0.81579080343, -0.475824400452)70.5806502498, 62.6483905439, 17.2741195888
5given(0.119283431819, -0.975126988332, 0.186812257413), (0.648559095602, 0.218991971437, 0.728981217836), (-0.751759644039, 0.03420340732, 0.658549591544)135.161370201, -12.1607226518, -19.8575936628
6given(-0.163663725147, 0.78763822281, 0.594003548003), (-0.7072603561, -0.513449140431, 0.485955521503), (0.687747754457, -0.340581869981, 0.641098288939)95.9080027502, 82.4697011177, 32.3778962215
7given(-0.611788507095, 0.742979702886, -0.271470041968), (0.748415824202, 0.432570140722, -0.50274926896), (-0.256102668222, -0.510748699906, -0.820699207307)116.266082346, -32.9799799697, 79.9682821027

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Components

#1: Protein
Aldehyde dehydrogenase 1A1 / 3-deoxyglucosone dehydrogenase / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / ...3-deoxyglucosone dehydrogenase / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / Aldehyde dehydrogenase / cytosolic / Retinal dehydrogenase 1 / RALDH 1 / RalDH1


Mass: 55363.477 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aldh1a1, Ahd-2, Ahd2, Aldh1 / Production host: Escherichia coli (E. coli)
References: UniProt: P24549, aminobutyraldehyde dehydrogenase, benzaldehyde dehydrogenase (NAD+), aldehyde dehydrogenase (NAD+), retinal dehydrogenase

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M potassium iodide (pH 7.0) and 20% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.89→127.96 Å / Num. obs: 85287 / % possible obs: 93.24 % / Redundancy: 1.9 % / Biso Wilson estimate: 69.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03502 / Rpim(I) all: 0.03502 / Rrim(I) all: 0.04952 / Net I/σ(I): 8.31
Reflection shellResolution: 2.89→2.995 Å / Rmerge(I) obs: 0.2951 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 9049 / CC1/2: 0.853 / Rpim(I) all: 0.2951 / Rrim(I) all: 0.4173

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2N

5l2n


Resolution: 2.89→127.96 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 2000 2.35 %
Rwork0.195 83246 -
obs0.1963 85246 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.11 Å2 / Biso mean: 76.2045 Å2 / Biso min: 28.52 Å2
Refinement stepCycle: final / Resolution: 2.89→127.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29957 0 0 0 29957
Num. residues----3950
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17880X-RAY DIFFRACTION14.585TORSIONAL
12B17880X-RAY DIFFRACTION14.585TORSIONAL
13C17880X-RAY DIFFRACTION14.585TORSIONAL
14D17880X-RAY DIFFRACTION14.585TORSIONAL
15E17880X-RAY DIFFRACTION14.585TORSIONAL
16F17880X-RAY DIFFRACTION14.585TORSIONAL
17G17880X-RAY DIFFRACTION14.585TORSIONAL
18H17880X-RAY DIFFRACTION14.585TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.960.34191510.263562906441100
2.96-3.040.30611520.250163206472100
3.04-3.130.29921530.239663726525100
3.13-3.240.3351530.244763596512100
3.24-3.350.30521520.2363106462100
3.35-3.480.31671090.22874565467471
3.49-3.610.26881200.21344985510599
3.7-3.840.2803970.21674056415395
3.84-4.080.22611510.18656290644199
4.08-4.390.21331520.17916306645899
4.39-4.830.2111510.15096318646999
4.83-5.530.24861530.17716384653799
5.53-6.970.23991530.20786345649899
6.97-127.960.21921530.17566346649998
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)
14.19220.73940.71343.40311.50553.37160.1458-1.05760.40130.643-0.13320.2459-0.2986-0.3180.09530.6417-0.06260.02710.6344-0.15460.442546.20637.619429.0014
22.1074-0.4285-0.62861.19170.19572.34910.0841-0.14080.29610.1343-0.0333-0.1687-0.40550.0148-0.06680.405-0.12-0.00420.296-0.02790.427549.962136.084513.8511
31.7339-0.64870.28021.12280.23532.65780.3377-0.1874-0.33110.2824-0.32910.04730.0183-0.6096-0.00110.4115-0.0093-0.03390.45930.00740.48531.055427.8252.5382
44.57710.296-0.55143.54541.07898.33440.1441-0.22990.03680.3387-0.78290.31690.4884-1.82410.60220.3334-0.1191-0.02251.00080.01050.713716.962121.08390.2037
52.26020.87951.16331.70261.08352.9184-0.034-0.65390.24720.1316-0.29470.6617-0.4789-1.08020.27140.50130.09220.10050.9406-0.1030.629118.95633.985211.3188
63.8368-1.1907-0.36711.8431.64485.98770.11280.13330.2763-0.1853-0.20540.1532-0.3631-0.47290.00090.3793-0.0006-0.03270.40880.0460.450825.028427.5597-8.0551
71.6930.26310.94730.233-0.02670.48540.1135-0.02460.30140.1675-0.1051-0.2224-0.27680.0126-0.03250.5409-0.1122-0.00770.43220.02590.528748.105728.6939-5.0826
81.70543.1496-0.09766.79961.82911.59650.2519-0.0916-0.02530.8965-0.09920.02470.54230.3219-0.13580.48380.102-0.12060.30690.02870.381167.7798-6.383419.5012
91.2232-0.78120.98141.0943-0.66921.31610.2819-0.0273-0.5215-0.1671-0.0160.19040.58130.0485-0.33040.55990.0221-0.12180.3171-0.07370.568465.0496-7.24329.1183
100.5411-0.29240.71980.3802-0.24661.57240.0780.08540.0327-0.0253-0.0146-0.02970.19650.2248-0.01040.4136-0.0244-0.03090.2802-0.05850.44564.76755.1256.9687
111.64050.8477-0.15932.1512-0.90160.61860.07240.20480.3233-0.03620.0325-0.6501-0.09770.6837-0.08460.4536-0.02810.06230.8122-0.12920.746588.221911.86354.4236
124.561.2033-1.83165.3946-0.20961.40690.12640.8647-0.1105-0.1485-0.0214-1.15860.11690.4541-0.02740.51070.1278-0.03871.1283-0.20180.989998.8361.2778.92
131.4267-2.0810.48792.2748-1.06892.45380.22520.39060.3111-0.587-0.1273-0.90850.2671.1086-0.03970.5537-0.1430.12581.1428-0.08940.850593.053616.654-5.0585
141.83370.8981-0.25540.69770.6350.7870.02-0.05950.1144-0.0035-0.0142-0.06070.16120.57570.02260.512-0.01190.0950.5669-0.010.606966.393615.2853-6.3346
151.9766-0.3610.6811.50640.40641.39750.28540.9086-0.1769-0.7703-0.0754-0.41190.03140.6177-0.16680.81180.24250.17131.0424-0.02040.656973.69188.4078-39.2447
161.7646-0.00810.91521.20840.42292.6150.25790.5632-0.132-0.3288-0.1485-0.22520.31690.6053-0.12370.51660.07360.09140.6121-0.00930.49466.809612.3501-28.3712
171.9766-0.29590.08111.38350.10312.24860.34120.3244-0.6958-0.2537-0.07610.30760.5917-0.1802-0.23120.73620.0166-0.15070.3588-0.05760.644542.7265-1.2156-25.3202
184.4513-0.3946-0.29882.04540.39170.61190.03770.868-0.9599-0.6767-0.13370.49630.55850.15990.12771.16250.2061-0.18950.7205-0.23310.73347.6541-9.6306-39.8385
192.04381.17820.65532.23830.10483.69940.1411-0.058-0.97790.0895-0.14140.0851.15430.34050.0260.66980.0334-0.09960.36820.06190.703942.777-4.7753-18.2449
200.01460.2229-0.13180.4581-0.24510.16680.45860.3864-0.0847-0.602-0.2676-0.07910.78230.3835-0.13330.76130.07210.03040.46750.07890.622253.30457.4527-20.0872
211.362-0.10750.12930.2456-0.59781.12850.0864-0.2281-0.07970.1943-0.1713-0.15430.23970.20060.05320.4444-0.04060.09860.4805-0.0190.623471.198522.978-5.8451
220.9911-0.87460.43192.9112-0.35221.0923-0.03240.36570.3325-1.0457-0.06610.0938-0.53820.23790.10470.9207-0.09-0.05380.45030.04490.478445.861351.0942-30.4591
231.1828-0.61940.66651.964-0.38712.0931-0.00010.3510.3584-0.2928-0.1207-0.271-0.45230.4330.11950.4693-0.07910.00310.37910.07810.414352.495941.6023-23.2334
242.308-0.6731.24712.1098-0.13491.2785-0.5908-0.3490.45810.06340.3869-0.4677-0.52410.38790.25540.7861-0.1341-0.08080.4610.01390.638257.751950.4497-6.582
251.632-1.14540.6851.1646-0.85732.1822-0.19580.42490.9427-0.025-0.139-0.9707-0.90450.85320.0721.1083-0.4559-0.06881.04020.27291.413875.592159.8961-15.9698
261.1219-0.8502-0.12142.9477-1.8851.6206-0.50220.43110.85420.20670.1355-0.8585-1.30360.29290.38951.2441-0.3016-0.03821.01550.17461.413572.992566.1811-12.4078
273.2479-2.541.11713.1456-1.20595.0537-0.2985-0.27021.3664-0.02080.1215-1.0051-1.38370.70510.2880.6105-0.23530.03520.6405-0.09851.019975.759250.76560.041
283.3587-0.62011.98830.73540.29592.0241-0.09040.42960.7707-0.56840.0337-0.2452-0.79740.21630.26490.645-0.22240.08740.73560.04310.792668.813442.4018-7.4642
292.318-0.16260.04310.8827-1.1211.72310.19420.0841-0.190.29030.11720.0097-0.18320.0772-0.1770.4901-0.0370.0070.308-0.08030.415545.870123.0831-7.1997
301.42940.1958-1.32223.5643-3.18195.0168-0.175-0.1695-0.9481-0.39930.18990.28731.0363-1.1855-0.04040.6676-0.3418-0.11171.08920.17130.911964.76194.893249.2292
311.8804-0.26881.73791.0446-0.13132.7590.0495-0.5129-0.38290.03870.09420.27050.2841-0.8931-0.15110.5124-0.20610.03880.74430.09240.406376.753112.287454.6501
322.1558-0.96281.48462.09680.05071.9926-0.2226-0.4869-0.02220.3630.09840.1213-0.4986-0.89170.17750.51680.0682-0.00170.7873-0.05640.514172.576229.81156.9104
332.948-0.51591.48961.91430.21863.7628-0.26750.5440.8987-0.62150.4422-0.0581-0.9696-0.49130.52531.03530.2603-0.15340.92350.06970.858570.131748.717239.7457
343.1720.7293-0.58423.9621-0.8642.73220.0421-0.47260.4962-0.0887-0.00610.9763-0.5037-1.2368-0.10080.6780.2121-0.09141.2334-0.07920.810156.419333.86143.0512
353.4943-0.44521.49442.25090.84461.9210.1218-0.66960.65470.3083-0.22780.1925-0.7321-0.7660.16190.82030.1914-0.03190.7317-0.02840.579174.1445.432551.7018
360.7714-0.67020.80161.7584-1.75872.5518-0.132-0.30470.22360.13780.16350.1466-0.1248-0.5303-0.0610.6395-0.0104-0.0420.596-0.05760.50989.709724.366161.4378
371.8859-0.5744-0.38272.7658-0.40113.9051-0.2492-0.42330.40520.26550.14930.0129-0.9944-0.51290.10480.67490.1183-0.10570.611-0.12310.684987.57845.50988.641
381.5033-0.17430.95490.9260.07093.2171-0.1761-0.42580.0430.11180.04710.1103-0.0901-0.40630.09450.4326-0.01840.01460.48330.00570.428293.11529.44582.823
392.2058-0.6658-0.44892.7102-1.48530.9385-0.3003-0.8878-0.13820.96750.01750.34790.4254-0.4580.22660.9056-0.0380.08441.0234-0.02130.538589.82318.802105.16
402.4166-0.3465-0.54241.82522.76585.0873-0.2351-0.0634-0.30790.3942-0.19410.55220.6436-0.99320.4640.651-0.1994-0.04070.65110.12070.616291.2976.38286.11
410.8457-0.4160.83081.337-1.08410.99340.009-0.21770.030.4158-0.0126-0.05350.1439-0.5524-0.05570.6822-0.1295-0.01810.64940.11770.626492.97726.46767.126
422.209-0.30340.09451.67520.11912.558-0.09590.18160.7866-0.03020.16-0.6732-0.81920.8235-0.11660.7404-0.2682-0.080.69340.04770.8066125.648336.123764.1016
431.7517-0.472-0.2945-0.29350.67381.22810.14230.60141.227-0.1492-0.2321-0.4856-1.33630.7867-0.01581.4844-0.379-0.06991.09880.4081.3848117.717253.245240.6133
441.2355-0.99251.34820.1164-0.30081.8116-0.15710.18570.58550.4931-0.139-0.1732-0.70810.43110.23040.9079-0.1780.05440.62130.10110.61107.393831.201852.4804
453.22530.3775-0.50233.6279-2.68882.7424-0.11591.4697-0.7385-0.24510.31750.05740.5187-0.5588-0.30490.6028-0.11710.02081.0354-0.17610.6186107.79093.284825.2019
461.4491-0.02480.23751.90420.80062.444-0.03860.54190.1615-0.14130.1256-0.2918-0.06070.4507-0.09330.3866-0.1477-0.01180.62970.0620.4185108.718513.055337.3904
471.8887-0.43650.75130.04970.62163.3420.19110.5388-0.70190.00470.046-0.2681.18590.5602-0.25540.88930.0958-0.16460.7085-0.13780.8148121.7507-7.507353.2002
483.0678-0.5120.95222.56941.88612.6450.29860.2535-0.35490.02660.0621-0.30050.42090.5662-0.35560.7448-0.0017-0.17360.53590.02140.5555124.75170.484163.8425
490.72340.32930.7840.7897-1.16641.4885-0.15610.3550.3327-0.31880.0788-0.06140.04380.30380.09660.5653-0.1606-0.02520.62940.08490.709108.783119.616354.6768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 36 )A8 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 261 )A37 - 261
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 305 )A262 - 305
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 329 )A306 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 404 )A330 - 404
6X-RAY DIFFRACTION6chain 'A' and (resid 405 through 436 )A405 - 436
7X-RAY DIFFRACTION7chain 'A' and (resid 437 through 501 )A437 - 501
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 36 )B8 - 36
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 81 )B37 - 81
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 247 )B82 - 247
11X-RAY DIFFRACTION11chain 'B' and (resid 248 through 347 )B248 - 347
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 384 )B348 - 384
13X-RAY DIFFRACTION13chain 'B' and (resid 385 through 446 )B385 - 446
14X-RAY DIFFRACTION14chain 'B' and (resid 447 through 501 )B447 - 501
15X-RAY DIFFRACTION15chain 'C' and (resid 8 through 81 )C8 - 81
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 261 )C82 - 261
17X-RAY DIFFRACTION17chain 'C' and (resid 262 through 327 )C262 - 327
18X-RAY DIFFRACTION18chain 'C' and (resid 328 through 384 )C328 - 384
19X-RAY DIFFRACTION19chain 'C' and (resid 385 through 454 )C385 - 454
20X-RAY DIFFRACTION20chain 'C' and (resid 455 through 479 )C455 - 479
21X-RAY DIFFRACTION21chain 'C' and (resid 480 through 501 )C480 - 501
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 81 )D8 - 81
23X-RAY DIFFRACTION23chain 'D' and (resid 82 through 247 )D82 - 247
24X-RAY DIFFRACTION24chain 'D' and (resid 248 through 283 )D248 - 283
25X-RAY DIFFRACTION25chain 'D' and (resid 284 through 364 )D284 - 364
26X-RAY DIFFRACTION26chain 'D' and (resid 365 through 407 )D365 - 407
27X-RAY DIFFRACTION27chain 'D' and (resid 408 through 436 )D408 - 436
28X-RAY DIFFRACTION28chain 'D' and (resid 437 through 479 )D437 - 479
29X-RAY DIFFRACTION29chain 'D' and (resid 480 through 501 )D480 - 501
30X-RAY DIFFRACTION30chain 'E' and (resid 8 through 36 )E8 - 36
31X-RAY DIFFRACTION31chain 'E' and (resid 37 through 229 )E37 - 229
32X-RAY DIFFRACTION32chain 'E' and (resid 230 through 305 )E230 - 305
33X-RAY DIFFRACTION33chain 'E' and (resid 306 through 328 )E306 - 328
34X-RAY DIFFRACTION34chain 'E' and (resid 329 through 384 )E329 - 384
35X-RAY DIFFRACTION35chain 'E' and (resid 385 through 454 )E385 - 454
36X-RAY DIFFRACTION36chain 'E' and (resid 455 through 501 )E455 - 501
37X-RAY DIFFRACTION37chain 'F' and (resid 8 through 81 )F8 - 81
38X-RAY DIFFRACTION38chain 'F' and (resid 82 through 329 )F82 - 329
39X-RAY DIFFRACTION39chain 'F' and (resid 330 through 384 )F330 - 384
40X-RAY DIFFRACTION40chain 'F' and (resid 385 through 454 )F385 - 454
41X-RAY DIFFRACTION41chain 'F' and (resid 455 through 501 )F455 - 501
42X-RAY DIFFRACTION42chain 'G' and (resid 10 through 261 )G10 - 261
43X-RAY DIFFRACTION43chain 'G' and (resid 262 through 436 )G262 - 436
44X-RAY DIFFRACTION44chain 'G' and (resid 437 through 501 )G437 - 501
45X-RAY DIFFRACTION45chain 'H' and (resid 8 through 36 )H8 - 36
46X-RAY DIFFRACTION46chain 'H' and (resid 37 through 261 )H37 - 261
47X-RAY DIFFRACTION47chain 'H' and (resid 262 through 384 )H262 - 384
48X-RAY DIFFRACTION48chain 'H' and (resid 385 through 446 )H385 - 446
49X-RAY DIFFRACTION49chain 'H' and (resid 447 through 501 )H447 - 501

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