[English] 日本語
Yorodumi
- PDB-2wtz: MurE ligase of Mycobacterium Tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wtz
TitleMurE ligase of Mycobacterium Tuberculosis
ComponentsUDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
KeywordsLIGASE / NUCLEOTIDE-BINDING / PEPTIDOGLYCAN SYNTHESIS / MURE / CELL SHAPE / CELL CYCLE / MYCOBACTERIUM TUBERCULOSIS / CELL WALL BIOGENESIS/DEGRADATION / ATP-BINDING / PEPTIDOGLYCAN / CELL DIVISION
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane ...UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UAG / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBasavannacharya, C. / Robertson, G. / Munshi, T. / Keep, N.H. / Bhakta, S.
CitationJournal: Tuberculosis(Edinb.) / Year: 2010
Title: ATP-Dependent Mure Ligase in Mycobacterium Tuberculosis: Biochemical and Structural Characterisation.
Authors: Basavannacharya, C. / Robertson, G. / Munshi, T. / Keep, N.H. / Bhakta, S.
History
DepositionSep 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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_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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,43412
Polymers221,8194
Non-polymers3,6168
Water0
1
A: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3593
Polymers55,4551
Non-polymers9042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3593
Polymers55,4551
Non-polymers9042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3593
Polymers55,4551
Non-polymers9042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3593
Polymers55,4551
Non-polymers9042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.920, 79.800, 82.920
Angle α, β, γ (deg.)111.09, 92.16, 93.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33D
14C
24A
34B
15C
25A
35B
16C
26A
36B
17C
27A
37B
18C
28A
38B
19C
29A
39B
110A
210B
310C
410D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 139
2111B1 - 139
3111C1 - 139
4111D1 - 139
1121A140 - 385
2121B140 - 385
3121C140 - 385
4121D140 - 385
1131A386 - 535
2131B386 - 535
3131D386 - 535
1141C386 - 408
2141A386 - 408
3141B386 - 408
1151C413 - 418
2151A413 - 418
3151B413 - 418
1161C429 - 436
2161A429 - 436
3161B429 - 436
1171C441 - 446
2171A441 - 446
3171B441 - 446
1181C454 - 464
2181A454 - 464
3181B454 - 464
1191C474 - 505
2191A474 - 505
3191B474 - 505
11101A1498 - 1499
21101B1498 - 1499
31101C1498 - 1499
41101D1498 - 1499

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

-
Components

#1: Protein
UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE / UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / MESO- ...UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / MESO-A2PM-ADDING ENZYME / UDP-N-ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE / UDP-MURNAC-TRIPEPTIDE SYNTHETASE


Mass: 55454.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28BPLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/PLYSS
References: UniProt: P65477, UniProt: P9WJL3*PLUS, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical
ChemComp-UAG / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE


Mass: 879.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H43N5O23P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.4 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.35 M MGCL2, 0.1 M TRIS PH 8.5, 16% PEG 8000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3→56.3 Å / Num. obs: 33536 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.4 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8C
Resolution: 3→74.16 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.873 / SU B: 39.066 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. THE THIRD DOMAINS OF CHAINS C AND D (379-535) ARE SIGNIFICANTLY DISORDERED AND ONLY PARTIALLY MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25107 1671 5 %RANDOM
Rwork0.19257 ---
obs0.19549 31855 91.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.96 Å2-1.78 Å2
2--1.61 Å21.22 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 3→74.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13772 0 236 0 14008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214235
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.98619450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32351901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53522.399542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.593151990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.815146
X-RAY DIFFRACTIONr_chiral_restr0.1650.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110820
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_it0.5221.59479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.999215060
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74434756
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0254.54390
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
11A743tight positional0.050.05
12B743tight positional0.050.05
13C743tight positional0.050.05
14D743tight positional0.050.05
21A1737tight positional0.060.05
22B1737tight positional0.060.05
23C1737tight positional0.060.05
24D1737tight positional0.060.05
31A802tight positional0.050.05
32B802tight positional0.060.05
33D802tight positional0.040.05
41C165tight positional0.040.05
42A165tight positional0.060.05
43B165tight positional0.050.05
51C43tight positional0.060.05
52A43tight positional0.050.05
53B43tight positional0.10.05
61C50tight positional0.030.05
62A50tight positional0.020.05
63B50tight positional0.020.05
71C44tight positional0.040.05
72A44tight positional0.060.05
73B44tight positional0.040.05
81C71tight positional0.030.05
82A71tight positional0.030.05
83B71tight positional0.030.05
91C223tight positional0.040.05
92A223tight positional0.040.05
93B223tight positional0.050.05
101A59tight positional0.050.05
102B59tight positional0.050.05
103C59tight positional0.040.05
104D59tight positional0.040.05
11A743tight thermal2.9720
12B743tight thermal2.4720
13C743tight thermal2.6420
14D743tight thermal2.4120
21A1737tight thermal3.0420
22B1737tight thermal2.3120
23C1737tight thermal3.6820
24D1737tight thermal2.5720
31A802tight thermal2.9420
32B802tight thermal2.9720
33D802tight thermal4.2720
41C165tight thermal7.5120
42A165tight thermal3.7420
43B165tight thermal4.6620
51C43tight thermal11.6920
52A43tight thermal3.5420
53B43tight thermal8.1920
61C50tight thermal2.6220
62A50tight thermal1.4820
63B50tight thermal1.8620
71C44tight thermal9.0820
72A44tight thermal6.3220
73B44tight thermal2.9320
81C71tight thermal6.8520
82A71tight thermal3.3520
83B71tight thermal3.9620
91C223tight thermal5.8720
92A223tight thermal4.520
93B223tight thermal3.4120
101A59tight thermal3.7720
102B59tight thermal2.4720
103C59tight thermal5.9220
104D59tight thermal3.4420
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 136 -
Rwork0.264 2463 -
obs--94.06 %
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)
11.44950.11840.62574.49180.33154.4265-0.2014-0.31910.0126-0.02940.0344-0.18490.01460.42810.1670.06120.0205-0.03420.20320.04920.077826.1364-4.1005-0.7816
22.59420.27350.65162.2717-0.12911.8381-0.0254-0.19640.16320.05690.04090.3180.0101-0.2166-0.01560.0358-0.00860.03570.0980.01070.0843-5.3959-1.6519-8.2842
37.39921.93841.43915.97571.59176.81820.0787-0.34660.84410.0772-0.34180.4023-0.5514-0.5280.26310.37270.10550.11710.1936-0.10810.2676-15.4626.375916.1924
42.4688-0.0431-0.25465.2182-1.17154.38480.11150.21070.0147-0.173-0.3449-0.52830.02880.59790.23340.18170.08640.08290.27130.10690.088627.4897-23.27220.9023
52.32820.1974-0.44962.0297-0.23951.91960.02840.18450.0453-0.06130.02010.3249-0.0085-0.1426-0.04850.11020.0044-0.04340.0902-0.00530.0641-3.5246-23.391932.2865
66.0216-1.22151.38086.13910.69237.00910.46320.2567-0.44170.0419-0.24670.14370.7631-0.1003-0.21660.4131-0.0195-0.20260.185-0.12750.2038-15.9283-31.59759.2402
72.1375-0.7853-0.10845.2764-2.01983.8731-0.1654-0.2340.21040.06470.26180.3861-0.2948-0.2841-0.09640.19370.0389-0.04150.0513-0.03370.1947-2.542629.5268-20.6883
82.175-1.01020.33482.3444-0.19452.1501-0.12910.10820.29360.1003-0.1176-0.3702-0.3550.4210.24670.1582-0.1599-0.0680.16790.06410.124627.809719.5355-24.251
93.7041-3.66473.67335.90192.341922.7182-0.04820.0645-0.09060.71590.236-0.62430.5598-0.4718-0.18790.9643-0.3909-0.61320.9641-0.36031.098641.039335.8668-6.7491
102.7952-0.39070.80763.782-1.18676.16960.08390.0172-0.3564-0.0479-0.01430.47810.0317-0.234-0.06960.1075-0.0038-0.00950.0255-0.04210.1667-1.371-53.589645.8799
112.01770.6341-0.10791.4819-0.02361.8665-0.04910.1293-0.1754-0.0452-0.1656-0.17930.16760.36550.21470.05410.08560.04140.18590.0780.09930.6574-45.274345.5446
129.3086-0.58755.33184.4792-1.200811.41480.06831.7195-2.3303-0.7388-0.0557-0.15170.38550.585-0.01250.55010.16130.33990.6177-0.3031.008538.8564-64.633228.9065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 139
2X-RAY DIFFRACTION2A140 - 378
3X-RAY DIFFRACTION3A379 - 533
4X-RAY DIFFRACTION4B26 - 139
5X-RAY DIFFRACTION5B140 - 378
6X-RAY DIFFRACTION6B379 - 533
7X-RAY DIFFRACTION7C24 - 139
8X-RAY DIFFRACTION8C140 - 378
9X-RAY DIFFRACTION9C379 - 505
10X-RAY DIFFRACTION10D26 - 139
11X-RAY DIFFRACTION11D140 - 378
12X-RAY DIFFRACTION12D379 - 527

+
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