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- PDB-3zxv: Crystal structure of Mycobacterium Tuberculosis Glutamine Synthet... -

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Basic information

Entry
Database: PDB / ID: 3zxv
TitleCrystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with tri-substituted imidazole inhibitor (4-(2-tert-butyl- 4-(6-methoxynaphthalen-2-yl)-1H-imidazol-5-yl)pyridin-2-amine) and L- methionine-S-sulfoximine phosphate
ComponentsGLUTAMINE SYNTHETASE 1
KeywordsLIGASE / NUCLEOTIDE-BINDING / TAUT STATE / RV2220 / MT2278 / GLNA1
Function / homology
Function and homology information


nitrogen utilization / positive regulation of plasminogen activation / cell wall / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization ...nitrogen utilization / positive regulation of plasminogen activation / cell wall / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding / extracellular region / ATP binding / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site ...Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MXI / L-METHIONINE-S-SULFOXIMINE PHOSPHATE / PHOSPHATE ION / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsNilsson, M.T. / Mowbray, S.L.
Citation
Journal: J.Med.Chem. / Year: 2012
Title: Trisubstituted Imidazoles as Mycobacterium Tuberculosis Glutamine Synthetase Inhibitors.
Authors: Gising, J. / Nilsson, M.T. / Odell, L.R. / Yahiaoui, S. / Lindh, M. / Iyer, H. / Sinha, A.M. / Srinivasa, B.R. / Larhed, M. / Mowbray, S.L. / Karlen, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of Mycobacterium Tuberculosis Glutamine Synthetase in Complex with a Transition-State Mimic Provides Functional Insights.
Authors: Krajewski, W.W. / Jones, T.A. / Mowbray, S.L.
#2: Journal: J.Mol.Biol. / Year: 2009
Title: Structural Basis for the Inhibition of Mycobacterium Tuberculosis Glutamine Synthetase by Novel ATP-Competitive Inhibitors.
Authors: Nilsson, M.T. / Krajewski, W.W. / Yellagunda, S. / Prabhumurthy, S. / Chamarahally, G.N. / Siddamadappa, C. / Srinivasa, B.R. / Yahiaoui, S. / Larhed, M. / Karlen, A. / Jones, T.A. / Mowbray, S.L.
History
DepositionAug 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,52448
Polymers327,5086
Non-polymers5,01642
Water19,8891104
1
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules

A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)665,04996
Polymers655,01712
Non-polymers10,03284
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area99110 Å2
ΔGint-1077.9 kcal/mol
Surface area168280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.590, 227.150, 201.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASPAA4 - 40212 - 410
21LYSLYSASPASPBB4 - 40212 - 410
31LYSLYSASPASPCC4 - 40212 - 410
41LYSLYSASPASPDD4 - 40212 - 410
51LYSLYSASPASPEE4 - 40212 - 410
61LYSLYSASPASPFF4 - 40212 - 410
12ILEILEVALVALAA416 - 478424 - 486
22ILEILEVALVALBB416 - 478424 - 486
32ILEILEVALVALCC416 - 478424 - 486
42ILEILEVALVALDD416 - 478424 - 486
52ILEILEVALVALEE416 - 478424 - 486
62ILEILEVALVALFF416 - 478424 - 486
13MXIMXIHOHHOHAG - WA501 - 2129
23MXIMXIHOHHOHBN - XA501 - 2181
33MXIMXIHOHHOHCU - YA501 - 2183
43MXIMXIHOHHOHDBA - ZA501 - 2188
53MXIMXIHOHHOHEIA - AB501 - 2184
63MXIMXIHOHHOHFPA - BB501 - 2169

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.517, 0.8508, -0.09346), (-0.8507, 0.4988, -0.1657), (-0.09437, 0.1652, 0.9817)-36.24, 32.65, -6.999
2given(-0.4398, 0.8498, -0.2904), (-0.8495, -0.4986, -0.1725), (-0.2914, 0.1709, 0.9412)-26.17, 80.91, -5.252
3given(-0.92, 0.000858, -0.3918), (-0.002355, -1, 0.003341), (-0.3918, 0.003997, 0.92)19.65, 96.2, 3.921
4given(-0.4419, -0.8483, -0.2918), (0.8458, -0.5024, 0.1796), (-0.2989, -0.1675, 0.9395)55.51, 63.55, 11.16
5given(0.5194, -0.8491, -0.09669), (0.8483, 0.4986, 0.178), (-0.1029, -0.1745, 0.9793)45.74, 15.37, 9.537

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
GLUTAMINE SYNTHETASE 1 / GLUTAMATE--AMMONIA LIGASE 1


Mass: 54584.730 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV
Description: E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE DEFICIENT (GLNE-)
Plasmid: PCR T7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745
References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase

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Non-polymers , 6 types, 1146 molecules

#2: Chemical
ChemComp-MXI / 4-(2-TERT-BUTYL-4-(6-METHOXYNAPHTHALEN-2-YL)-3H-IMIDAZOL-4-YL)PYRIDIN-2-AMINE


Mass: 372.463 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H24N4O
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE


Mass: 260.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H13N2O6PS
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE ...PROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE PURIFICATION TAG.

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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: 2.32 Å3/Da / Density % sol: 47 %
Description: PROTEIN ONLY COORDINATES FROM THE ISOMORPHOUS CRYSTAL FORM FOUND IN PDB ENTRY 2BVC WERE USED AS THE STARTING POINT FOR REFINEMENT.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M MES, PH 6.8, 0.2 M MAGNESIUM CHLORIDE, 45% (V/V) PEG400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M ...Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M MES, PH 6.8, 0.2 M MAGNESIUM CHLORIDE, 45% (V/V) PEG400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M MAGNESIUM CHLORIDE, 4%(V/V) DMSO, 0.001 M INHIBITOR, 0.004 M MSOP), HANGING-DROP, VAPOR DIFFUSION, TEMPERATURE 294K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0683
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0683 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. obs: 140955 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 38.993 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 2.26→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.29 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVC

2bvc


Resolution: 2.26→29.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.346 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.357 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 403-415 ARE EXCLUDED FROM THE NCS DUE TO DIFFERENCES AS A RESULT OF CRYSTAL CONTACTS
RfactorNum. reflection% reflectionSelection details
Rfree0.21055 7110 5 %RANDOM
Rwork0.19505 ---
obs0.19584 133842 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---2.48 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22572 0 312 1104 23988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02223502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.96731992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95152844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40824.1971158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86153624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.88515126
X-RAY DIFFRACTIONr_chiral_restr0.0840.23324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118516
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4261.514268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.834223004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28139234
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1124.58988
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3132tight positional0.040.05
12B3132tight positional0.040.05
13C3132tight positional0.030.05
14D3132tight positional0.030.05
15E3132tight positional0.040.05
16F3132tight positional0.030.05
21A528tight positional0.030.05
22B528tight positional0.030.05
23C528tight positional0.030.05
24D528tight positional0.030.05
25E528tight positional0.040.05
26F528tight positional0.030.05
31A236tight positional0.060.05
32B236tight positional0.070.05
33C236tight positional0.060.05
34D236tight positional0.070.05
35E236tight positional0.070.05
36F236tight positional0.060.05
11A3132tight thermal0.090.5
12B3132tight thermal0.10.5
13C3132tight thermal0.090.5
14D3132tight thermal0.090.5
15E3132tight thermal0.10.5
16F3132tight thermal0.10.5
21A528tight thermal0.080.5
22B528tight thermal0.080.5
23C528tight thermal0.080.5
24D528tight thermal0.080.5
25E528tight thermal0.10.5
26F528tight thermal0.080.5
31A236tight thermal0.150.5
32B236tight thermal0.150.5
33C236tight thermal0.150.5
34D236tight thermal0.140.5
35E236tight thermal0.160.5
36F236tight thermal0.130.5
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 520 -
Rwork0.289 9710 -
obs--98.5 %

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