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- PDB-5dn6: ATP synthase from Paracoccus denitrificans -

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Basic information

Entry
Database: PDB / ID: 5dn6
TitleATP synthase from Paracoccus denitrificans
Components
  • (ATP synthase ...) x 7
  • Chain A
  • Chain B
  • Chain C
  • Chain V
  • Chain W
  • Chain Y
  • Zeta inhibitor protein
KeywordsHYDROLASE / Paracoccus denitrificans / ATP synthase / complex / regulation / proton translocation
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / molecular function inhibitor activity / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / lipid binding / ATP binding / plasma membrane
Similarity search - Function
ATPase inhibitor subunit zeta / ATPase inhibitor subunit zeta superfamily / ATPase inhibitor subunit zeta / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin ...ATPase inhibitor subunit zeta / ATPase inhibitor subunit zeta superfamily / ATPase inhibitor subunit zeta / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DUF1476 domain-containing protein / ATP synthase subunit c / ATP synthase subunit a / ATP synthase subunit delta / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 Å
AuthorsMorales-Rios, E. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (United Kingdom)U105663150 United Kingdom
Medical Research Council (United Kingdom)U105184325 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 angstrom resolution.
Authors: Morales-Rios, E. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Other
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 4, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_ins_code ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Dec 4, 2019Group: Source and taxonomy / Structure summary / Category: entity / entity_name_com / entity_src_nat
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.strain
Revision 2.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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
1: Chain A
2: Chain B
3: Chain C
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase subunit delta
I: ATP synthase epsilon chain
J: ATP synthase F0 subcomplex C subunit
K: ATP synthase F0 subcomplex C subunit
L: ATP synthase F0 subcomplex C subunit
M: ATP synthase F0 subcomplex C subunit
N: ATP synthase F0 subcomplex C subunit
O: ATP synthase F0 subcomplex C subunit
P: ATP synthase F0 subcomplex C subunit
Q: ATP synthase F0 subcomplex C subunit
R: ATP synthase F0 subcomplex C subunit
S: ATP synthase F0 subcomplex C subunit
T: ATP synthase F0 subcomplex C subunit
U: ATP synthase F0 subcomplex C subunit
V: Chain V
W: Chain W
X: ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a
Y: Chain Y
Z: Zeta inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,79539
Polymers543,21829
Non-polymers2,57710
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.001, 187.943, 164.724
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11J
21K
31L
41M
51N
61O
71P
81Q
91R
101S
111T
121U

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNARGARGJM3 - 403 - 40
21ASNASNARGARGKN3 - 403 - 40
31ASNASNARGARGLO3 - 403 - 40
41ASNASNARGARGMP3 - 403 - 40
51ASNASNARGARGNQ3 - 403 - 40
61ASNASNARGARGOR3 - 403 - 40
71ASNASNARGARGPS3 - 403 - 40
81ASNASNARGARGQT3 - 403 - 40
91ASNASNARGARGRU3 - 403 - 40
101ASNASNARGARGSV3 - 403 - 40
111ASNASNARGARGTW3 - 403 - 40
121ASNASNARGARGUX3 - 403 - 40
12ALAALAPHEPHEJM45 - 7545 - 75
22ALAALAPHEPHEKN45 - 7545 - 75
32ALAALAPHEPHELO45 - 7545 - 75
42ALAALAPHEPHEMP45 - 7545 - 75
52ALAALAPHEPHENQ45 - 7545 - 75
62ALAALAPHEPHEOR45 - 7545 - 75
72ALAALAPHEPHEPS45 - 7545 - 75
82ALAALAPHEPHEQT45 - 7545 - 75
92ALAALAPHEPHERU45 - 7545 - 75
102ALAALAPHEPHESV45 - 7545 - 75
112ALAALAPHEPHETW45 - 7545 - 75
122ALAALAPHEPHEUX45 - 7545 - 75

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.916927, -0.367699, -0.155059), (0.317523, 0.907613, -0.274625), (0.241713, 0.202576, 0.948967)14.05834, -19.83484, -21.42646
3given(0.655071, -0.730789, -0.191911), (0.523001, 0.621878, -0.582869), (0.5453, 0.281451, 0.789578)40.3602, -26.99397, -43.78447
4given(0.313738, -0.946265, -0.078433), (0.52962, 0.242959, -0.812695), (0.78808, 0.213434, 0.577387)68.36225, -18.94399, -58.9228
5given(-0.07345, -0.985506, 0.152916), (0.340932, -0.168905, -0.92479), (0.937214, -0.015792, 0.348396)95.58798, 3.48685, -63.47226
6given(-0.352306, -0.817422, 0.455742), (-0.006203, -0.484914, -0.87454), (0.935864, -0.310933, 0.165767)110.51236, 34.36644, -56.5378
7given(-0.467878, -0.495636, 0.731735), (-0.402277, -0.617777, -0.675666), (0.786933, -0.610489, 0.089661)110.9349, 63.9222, -39.39861
8given(-0.383453, -0.058213, 0.921724), (-0.766481, -0.536715, -0.352767), (0.515239, -0.841753, 0.161186)95.39314, 87.10921, -15.20301
9given(-0.102885, 0.299134, 0.948648), (-0.97092, -0.237461, -0.030423), (0.216167, -0.924192, 0.314867)68.06116, 94.24289, 6.99018
10given(0.241481, 0.521419, 0.818419), (-0.970172, 0.148236, 0.191815), (-0.021304, -0.840326, 0.541662)39.32816, 84.7783, 21.19021
11given(0.617043, 0.544069, 0.568548), (-0.768566, 0.571828, 0.286914), (-0.169011, -0.614005, 0.770995)13.44234, 61.40098, 25.74531
12given(0.893223, 0.353629, 0.277667), (-0.417441, 0.881674, 0.219984), (-0.167019, -0.312404, 0.935151)-0.95802, 30.65183, 18.44608

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Components

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Protein/peptide , 3 types, 3 molecules 123

#1: Protein/peptide Chain A


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
#2: Protein/peptide Chain B


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
#3: Protein/peptide Chain C


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)

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ATP synthase ... , 7 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUX

#4: Protein ATP synthase subunit alpha / / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55099.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
References: UniProt: A1B8N8, H+-transporting two-sector ATPase
#5: Protein ATP synthase subunit beta / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50385.977 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
References: UniProt: A1B8P0, H+-transporting two-sector ATPase
#6: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31639.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B8N9
#7: Protein ATP synthase subunit delta / / ATP synthase F(1) sector subunit delta / F-type ATPase subunit delta / F-ATPase subunit delta


Mass: 20047.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B8N7
#8: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 15840.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B8P1
#9: Protein
ATP synthase F0 subcomplex C subunit


Mass: 7610.894 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B618
#12: Protein ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a / / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 29724.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The UNK residues actually appear earlier than the proper residues listed. We used higher numbers so people would not mis-assign them.,The UNK residues actually appear earlier than the proper ...Details: The UNK residues actually appear earlier than the proper residues listed. We used higher numbers so people would not mis-assign them.,The UNK residues actually appear earlier than the proper residues listed. We used higher numbers so people would not mis-assign them.,The UNK residues actually appear earlier than the proper residues listed. We used higher numbers so people would not mis-assign them.,The UNK residues actually appear earlier than the proper residues listed. We used higher numbers so people would not mis-assign them.
Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B619

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Protein , 4 types, 4 molecules VWYZ

#10: Protein Chain V


Mass: 6656.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
#11: Protein Chain W


Mass: 10571.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
#13: Protein Chain Y


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria)
#14: Protein Zeta inhibitor protein


Mass: 11686.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: A1B602

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Non-polymers , 3 types, 10 molecules

#15: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 50 mM Tris-HCl pH 8.0, 70-100 mM MgCl2, 18-20% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 3.97→36.84 Å / Num. obs: 57347 / % possible obs: 98.3 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.253 / Net I/σ(I): 7.7
Reflection shellResolution: 3.97→4.08 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.604 / Mean I/σ(I) obs: 1.9 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.98→36.84 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.827 / SU B: 73.939 / SU ML: 0.965 / Cross valid method: THROUGHOUT / ESU R Free: 1.002 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32414 2791 4.9 %RANDOM
Rwork0.29546 ---
obs0.29686 54496 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.21 Å2
Baniso -1Baniso -2Baniso -3
1--4.49 Å20 Å2-6.62 Å2
2--1.48 Å20 Å2
3---4.58 Å2
Refinement stepCycle: 1 / Resolution: 3.98→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31374 0 156 0 31530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0232077
X-RAY DIFFRACTIONr_bond_other_d0.0030.0229653
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.96743360
X-RAY DIFFRACTIONr_angle_other_deg0.962367347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.89854641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27324.5811037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.225154223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.22215174
X-RAY DIFFRACTIONr_chiral_restr0.0670.25223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0238121
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.08816.84718913
X-RAY DIFFRACTIONr_mcbond_other3.08816.84618912
X-RAY DIFFRACTIONr_mcangle_it5.47625.21123286
X-RAY DIFFRACTIONr_mcangle_other5.47625.21223287
X-RAY DIFFRACTIONr_scbond_it1.95613.77213164
X-RAY DIFFRACTIONr_scbond_other1.95613.77213165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.84821.19820075
X-RAY DIFFRACTIONr_long_range_B_refined13.263105033
X-RAY DIFFRACTIONr_long_range_B_other13.263105034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
J163medium positional00.5
K163medium positional00.5
L163medium positional00.5
M163medium positional00.5
N163medium positional00.5
O163medium positional00.5
P163medium positional00.5
Q163medium positional00.5
R163medium positional00.5
S163medium positional00.5
T163medium positional00.5
U163medium positional00.5
J401tight thermal23.960.5
K401tight thermal32.510.5
L401tight thermal32.190.5
M401tight thermal24.20.5
N401tight thermal32.430.5
O401tight thermal44.750.5
P401tight thermal19.950.5
Q401tight thermal40.590.5
R401tight thermal21.670.5
S401tight thermal35.750.5
T401tight thermal24.330.5
U401tight thermal21.930.5
J163medium thermal24.022
K163medium thermal31.572
L163medium thermal32.572
M163medium thermal23.372
N163medium thermal32.052
O163medium thermal45.532
P163medium thermal19.942
Q163medium thermal39.542
R163medium thermal20.432
S163medium thermal34.92
T163medium thermal23.652
U163medium thermal22.442
LS refinement shellResolution: 3.978→4.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 194 -
Rwork0.357 3758 -
obs--93.19 %

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