[English] 日本語
Yorodumi
- PDB-2bx9: Crystal structure of B.subtilis Anti-TRAP protein, an antagonist ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bx9
TitleCrystal structure of B.subtilis Anti-TRAP protein, an antagonist of TRAP-RNA interactions
ComponentsTRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
KeywordsTRANSCRIPTION REGULATION / ANTI-TRAP
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Chaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Other non-globular / Special
Similarity search - Domain/homology
Tryptophan RNA-binding attenuator protein inhibitory protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsShevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal Structure of Bacillus Subtilis Anti-Trap Protein, an Antagonist of Trap/RNA Interaction.
Authors: Shevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.
History
DepositionJul 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
B: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
C: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
D: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
E: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
F: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
G: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
H: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
I: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
J: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
K: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
L: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,65224
Polymers67,86712
Non-polymers78512
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22260 Å2
ΔGint-181.9 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.552, 60.125, 60.348
Angle α, β, γ (deg.)113.99, 101.37, 100.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALCYSCYS3AA2 - 122 - 12
21VALVALCYSCYS3BB2 - 122 - 12
31VALVALCYSCYS3CC2 - 122 - 12
41VALVALCYSCYS3DD2 - 122 - 12
51VALVALCYSCYS3EE2 - 122 - 12
61VALVALCYSCYS3FF2 - 122 - 12
71VALVALCYSCYS3GG2 - 122 - 12
81VALVALCYSCYS3HH2 - 122 - 12
91VALVALCYSCYS3II2 - 122 - 12
101VALVALCYSCYS3JJ2 - 122 - 12
111VALVALCYSCYS3KK2 - 122 - 12
121VALVALCYSCYS3LL2 - 122 - 12
12PROPROLYSLYS2AA13 - 3213 - 32
22PROPROLYSLYS2BB13 - 3213 - 32
32PROPROLYSLYS2CC13 - 3213 - 32
42PROPROLYSLYS2DD13 - 3213 - 32
52PROPROLYSLYS2EE13 - 3213 - 32
62PROPROLYSLYS2FF13 - 3213 - 32
72PROPROLYSLYS2GG13 - 3213 - 32
82PROPROLYSLYS2HH13 - 3213 - 32
92PROPROLYSLYS2II13 - 3213 - 32
102PROPROLYSLYS2JJ13 - 3213 - 32
112PROPROLYSLYS2KK13 - 3213 - 32
122PROPROLYSLYS2LL13 - 3213 - 32
13GLYGLYASNASN3AA33 - 5233 - 52
23GLYGLYASNASN3BB33 - 5233 - 52
33GLYGLYASNASN3CC33 - 5233 - 52
43GLYGLYASNASN3DD33 - 5233 - 52
53GLYGLYASNASN3EE33 - 5233 - 52
63GLYGLYASNASN3FF33 - 5233 - 52
73GLYGLYASNASN3GG33 - 5233 - 52
83GLYGLYASNASN3HH33 - 5233 - 52
93GLYGLYASNASN3II33 - 5233 - 52
103GLYGLYASNASN3JJ33 - 5233 - 52
113GLYGLYASNASN3KK33 - 5233 - 52
123GLYGLYASNASN3LL33 - 5233 - 52

-
Components

#1: Protein
TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN / ANTI-TRAP / AT


Mass: 5655.565 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET17AT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: O31466
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: CONDITIONS: 21-23 % (W/V) POLY(ETHYLENE) GLYCOL 5000 MONMETHYL ETHER; 0.1 M SODIUM CACODYLATE PH 6.5; 50 MM MAGNESIUM ACETATE CRYOSOLUTION: 16 % GLYCEROL (V/V) WITH HIGHER CONCENTRATION OF POLY(ETHYLENE) GLYCOL

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 1.28258
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 27, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.282581
ReflectionResolution: 2.8→20 Å / Num. obs: 14370 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.4 / % possible all: 83

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0013refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.85 / SU B: 41.427 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.296 724 5 %RANDOM
Rwork0.192 ---
obs0.197 13637 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å2-0.07 Å20.48 Å2
2--0.68 Å20.59 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 12 130 4834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9896487
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.145624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.5326.433171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12415855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9781512
X-RAY DIFFRACTIONr_chiral_restr0.090.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023448
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.22175
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.04323239
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75235055
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.89361728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.986101432
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

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A204tight positional0.350.2
2B204tight positional0.390.2
3C204tight positional0.270.2
4D204tight positional0.640.2
5E204tight positional0.480.2
6F204tight positional0.750.2
7G204tight positional0.430.2
8H204tight positional0.790.2
9I204tight positional0.850.2
10J204tight positional0.40.2
11K204tight positional0.270.2
12L204tight positional0.270.2
1A58medium positional1.442
2B58medium positional1.132
3C58medium positional1.192
4D58medium positional1.672
5E58medium positional1.042
6F58medium positional1.842
7G58medium positional1.182
8H58medium positional1.862
9I58medium positional1.932
10J58medium positional1.542
11K58medium positional0.882
12L58medium positional1.312
1A102loose positional0.610.5
2B102loose positional0.740.5
3C102loose positional0.580.5
4D102loose positional0.690.5
5E102loose positional0.620.5
6F102loose positional1.080.5
7G102loose positional0.770.5
8H102loose positional0.990.5
9I102loose positional1.090.5
10J102loose positional0.740.5
11K102loose positional0.640.5
12L102loose positional0.60.5
1A204tight thermal0.482
2B204tight thermal0.392
3C204tight thermal0.422
4D204tight thermal0.62
5E204tight thermal0.522
6F204tight thermal0.572
7G204tight thermal0.572
8H204tight thermal0.492
9I204tight thermal0.642
10J204tight thermal0.422
11K204tight thermal0.612
12L204tight thermal0.442
1A58medium thermal3.1910
2B58medium thermal2.4510
3C58medium thermal2.1910
4D58medium thermal3.9210
5E58medium thermal2.7310
6F58medium thermal2.6210
7G58medium thermal3.7710
8H58medium thermal2.710
9I58medium thermal3.5410
10J58medium thermal2.0710
11K58medium thermal3.8910
12L58medium thermal1.8810
1A102loose thermal4.1210
2B102loose thermal3.8610
3C102loose thermal3.3510
4D102loose thermal2.8310
5E102loose thermal3.8910
6F102loose thermal3.6510
7G102loose thermal3.7310
8H102loose thermal3.0810
9I102loose thermal3.6410
10J102loose thermal2.9510
11K102loose thermal3.3910
12L102loose thermal3.4410
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.404 99 -
Rwork0.253 1792 -
obs--87.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.19590.31173.22728.5286-4.997616.5780.0824-0.4524-0.2812-0.28440.2591-0.4-0.04260.7134-0.3416-0.3109-0.04680.0416-0.09670.0021-0.032622.382728.022929.5824
218.88923.1639-11.194423.9297-4.637617.01430.18670.3699-0.6912-1.8703-0.806-1.58150.61060.86410.6192-0.0697-0.00080.20110.00450.09-0.077426.451636.603912.211
34.7968-2.2956-3.2579.76654.014614.8156-0.25090.40280.53350.3240.1978-0.9286-0.05830.35180.0531-0.3402-0.00520.0588-0.00820.0562-0.057522.763421.806136.1214
421.04479.411211.67498.11961.842913.95220.9429-0.57480.25090.7149-0.1788-1.6522-1.73972.3538-0.76410.1556-0.3494-0.0580.4705-0.20260.178327.462431.681751.6252
53.07860.32211.420111.9517-0.870210.8228-0.483-0.2263-0.1316-0.0160.3609-1.07770.33750.67690.1221-0.31710.06120.0699-0.0491-0.0115-0.094222.253719.679827.2334
627.8518-29.7238.499132.8031-3.689629.31940.82520.738-2.31060.04220.6072-0.79422.60772.9916-1.43240.43670.2104-0.180.25110.00370.626425.63540.89428.9207
715.0498-4.4953.04798.624-1.43015.4015-0.1879-0.0690.22080.94520.1108-0.2748-0.45590.01450.0771-0.2827-0.0615-0.0135-0.2531-0.0675-0.32444.115928.718848.0294
810.72151.84960.23686.0684-1.67726.2220.1308-0.6287-0.63770.8668-0.6219-0.8671-1.15711.67750.4912-0.1069-0.0805-0.1573-0.10660.0455-0.103318.825923.408459.9705
95.83510.71310.276917.7211-5.74169.27790.2444-0.20030.05910.4343-0.35050.28680.1934-0.15510.1061-0.36810.08160.0239-0.2817-0.1048-0.3269-4.20528.908644.7566
1015.5349-7.1831-1.37220.11267.123110.7918-0.6971-0.7590.98290.70240.4048-0.4687-0.91290.1330.29230.0440.1594-0.2036-0.2389-0.13510.0136-7.81348.11145.6516
118.59724.94683.791611.13893.185311.81410.0907-0.49560.17330.4687-0.1450.0802-0.0595-0.16450.0543-0.32080.10130.0779-0.2887-0.0356-0.3697-0.682821.1547.5956
1227.44826.9394-6.096410.0838-6.232310.58970.4611-1.12760.09620.8077-0.06490.92920.3321-1.2958-0.3962-0.13010.00560.01530.03470.0848-0.0389-17.79749.924847.3077
137.36561.7658-0.37968.34684.886510.26980.0865-0.11220.0965-0.3609-0.1862-0.0805-1.1121-0.07170.0997-0.146-0.0318-0.0157-0.25080.1949-0.2983-4.591132.140619.1533
142.3963-2.66822.59756.9882-5.869332.4298-0.50881.0821-0.0342-0.47590.69230.61410.0187-3.1905-0.1834-0.1674-0.1661-0.04350.41410.0057-0.1753-8.898723.25592.1873
159.1953-0.0541-4.70734.01384.698712.0990.0538-0.29390.6903-0.60150.19670.2506-0.81150.1623-0.2505-0.014-0.0132-0.0401-0.24750.0395-0.2701-1.46437.841825.6535
1617.5474-6.8381-8.13289.17492.56054.707-0.0131-0.5991.442-0.7995-0.40551.2655-0.6055-0.67250.41860.09690.2219-0.17680.0635-0.22270.1851-17.12344.156735.8206
1714.2754-0.02453.05044.54280.206310.74310.0025-0.06750.3448-0.59370.30510.2113-0.68730.3512-0.3076-0.1007-0.0899-0.0091-0.22610.1098-0.20654.312235.058318.0846
188.85899.8891-2.271829.7451-4.667612.79940.4837-0.30961.01890.0466-0.4341-0.1982-0.5893-0.0776-0.0496-0.2111-0.0811-0.0482-0.16260.0321-0.045719.881648.039218.6392
1911.15083.2881-2.17249.0078-1.31767.7455-0.09630.6359-0.0917-0.41610.1488-0.00440.79510.0662-0.0525-0.0557-0.0569-0.0068-0.2935-0.0172-0.27643.62015.619627.2723
2010.5002-13.0242-5.429519.96929.943515.23521.00051.36-0.1301-1.6839-1.3308-0.27681.90120.07590.33030.43660.07580.19760.3188-0.08770.063418.7705-1.80216.8218
212.20410.3832-0.18365.91180.209515.3347-0.10750.3004-0.1035-0.70950.46410.0733-0.2060.3606-0.3566-0.1577-0.11190.0085-0.3369-0.0263-0.1852-4.79568.158728.6584
229.40224.4138-3.140414.6532-3.68996.8367-0.4094-0.2775-0.3503-0.01010.41870.30551.0821-0.0805-0.0092-0.14390.11320.0803-0.2737-0.0235-0.1893-9.0413-1.666145.7213
2310.6317-6.81641.970712.4038-7.408911.0656-0.23790.4074-0.72870.0433-0.06390.9829-0.01110.22530.3018-0.0993-0.18920.0259-0.3135-0.0218-0.2744-1.04549.661620.8789
2470.519313.920227.229330.4576-6.315115.4457-0.30352.9482-1.5399-0.67922.98943.97111.1429-1.5405-2.68590.0162-0.3131-0.24310.49340.24930.5383-15.306214.64512.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION1A36 - 53
3X-RAY DIFFRACTION2A10 - 35
4X-RAY DIFFRACTION3B1 - 9
5X-RAY DIFFRACTION3B36 - 53
6X-RAY DIFFRACTION4B10 - 35
7X-RAY DIFFRACTION5C1 - 9
8X-RAY DIFFRACTION5C36 - 53
9X-RAY DIFFRACTION6C10 - 35
10X-RAY DIFFRACTION7D1 - 9
11X-RAY DIFFRACTION7D36 - 53
12X-RAY DIFFRACTION8D10 - 35
13X-RAY DIFFRACTION9E1 - 9
14X-RAY DIFFRACTION9E36 - 53
15X-RAY DIFFRACTION10E10 - 35
16X-RAY DIFFRACTION11F1 - 9
17X-RAY DIFFRACTION11F36 - 53
18X-RAY DIFFRACTION12F10 - 35
19X-RAY DIFFRACTION13G1 - 9
20X-RAY DIFFRACTION13G36 - 53
21X-RAY DIFFRACTION14G10 - 35
22X-RAY DIFFRACTION15H1 - 9
23X-RAY DIFFRACTION15H36 - 53
24X-RAY DIFFRACTION16H10 - 35
25X-RAY DIFFRACTION17I1 - 9
26X-RAY DIFFRACTION17I36 - 53
27X-RAY DIFFRACTION18I10 - 35
28X-RAY DIFFRACTION19J1 - 9
29X-RAY DIFFRACTION19J36 - 53
30X-RAY DIFFRACTION20J10 - 35
31X-RAY DIFFRACTION21K1 - 9
32X-RAY DIFFRACTION21K36 - 53
33X-RAY DIFFRACTION22K10 - 35
34X-RAY DIFFRACTION23L1 - 9
35X-RAY DIFFRACTION23L36 - 53
36X-RAY DIFFRACTION24L10 - 35

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more