[English] 日本語
Yorodumi
- PDB-6b2o: LarE, a sulfur transferase involved in synthesis of the cofactor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b2o
TitleLarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant
ComponentsATP-utilizing enzyme of the PP-loopsuperfamily
KeywordsTRANSFERASE / Lar / sulfur transferase / LarE / AMPylation / hexamer / trimer / PP-loop / ATP / magnesium / ATP pyrophophatase domain / lactate / lactate racemization / lactate racemase / cysteine to alanine
Function / homology
Function and homology information


pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase / NAD+ synthase (glutamine-hydrolysing) / sulfurtransferase activity / NAD+ synthase (glutamine-hydrolyzing) activity / lyase activity / ATP binding
Similarity search - Function
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase LarE / : / NAD/GMP synthase / NAD synthase / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent sacrificial sulfur transferase LarE / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsFellner, M. / Hausinger, R.P. / Hu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1516126 United States
CitationJournal: Biochemistry / Year: 2018
Title: Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum.
Authors: Fellner, M. / Rankin, J.A. / Desguin, B. / Hu, J. / Hausinger, R.P.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-utilizing enzyme of the PP-loopsuperfamily
B: ATP-utilizing enzyme of the PP-loopsuperfamily
C: ATP-utilizing enzyme of the PP-loopsuperfamily
D: ATP-utilizing enzyme of the PP-loopsuperfamily
E: ATP-utilizing enzyme of the PP-loopsuperfamily
F: ATP-utilizing enzyme of the PP-loopsuperfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,17017
Polymers190,1206
Non-polymers1,05011
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-65 kcal/mol
Surface area63850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.660, 108.660, 328.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-495-

HOH

21B-529-

HOH

31E-445-

HOH

41E-451-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 6 or (resid 7...
21(chain B and (resid 5 through 6 or (resid 7...
31(chain C and (resid 5 through 6 or (resid 7...
41(chain D and (resid 5 through 43 or (resid 44...
51(chain E and (resid 5 through 6 or (resid 7...
61(chain F and (resid 5 through 6 or (resid 7...

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
11ALAALATHRTHR(chain A and (resid 5 through 6 or (resid 7...AA5 - 65 - 6
12LYSLYSALAALA(chain A and (resid 5 through 6 or (resid 7...AA7 - 97 - 9
13ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
14ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
15ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
16ALAALAALAALA(chain A and (resid 5 through 6 or (resid 7...AA2 - 2762 - 276
21ALAALATHRTHR(chain B and (resid 5 through 6 or (resid 7...BB5 - 65 - 6
22LYSLYSALAALA(chain B and (resid 5 through 6 or (resid 7...BB7 - 97 - 9
23ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
24ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
25ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
26ALAALAARGARG(chain B and (resid 5 through 6 or (resid 7...BB2 - 2592 - 259
31ALAALATHRTHR(chain C and (resid 5 through 6 or (resid 7...CC5 - 65 - 6
32LYSLYSALAALA(chain C and (resid 5 through 6 or (resid 7...CC7 - 97 - 9
33ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
34ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
35ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
36ALAALAARGARG(chain C and (resid 5 through 6 or (resid 7...CC2 - 2592 - 259
41ALAALAGLYGLY(chain D and (resid 5 through 43 or (resid 44...DD5 - 435 - 43
42ARGARGARGARG(chain D and (resid 5 through 43 or (resid 44...DD4444
43ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
44ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
45ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
46ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
47ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
48ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
49ALAALAARGARG(chain D and (resid 5 through 43 or (resid 44...DD5 - 2595 - 259
51ALAALATHRTHR(chain E and (resid 5 through 6 or (resid 7...EE5 - 65 - 6
52LYSLYSALAALA(chain E and (resid 5 through 6 or (resid 7...EE7 - 97 - 9
53ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
54ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
55ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
56ALAALATRPTRP(chain E and (resid 5 through 6 or (resid 7...EE2 - 2792 - 279
61ALAALATHRTHR(chain F and (resid 5 through 6 or (resid 7...FF5 - 65 - 6
62LYSLYSALAALA(chain F and (resid 5 through 6 or (resid 7...FF7 - 97 - 9
63ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
64ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
65ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260
66ALAALASERSER(chain F and (resid 5 through 6 or (resid 7...FF2 - 2602 - 260

-
Components

#1: Protein
ATP-utilizing enzyme of the PP-loopsuperfamily / Lactate racemization operon protein LarE / PP-loop superfamily ATP-binding protein / TIGR00268 family protein


Mass: 31686.703 Da / Num. of mol.: 6 / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria)
Gene: A8P51_04975, AVR82_02840, BIZ32_00440, IV39_GL000116, LPJSA22_00116, Nizo1839_0768, Nizo2891_3302, SRCM101060_01452
Plasmid: pGIR076-C176A / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express DE3 / References: UniProt: A0A0G9FES3, UniProt: F9UST4*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.79 % / Mosaicity: 0.17 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 ul 8 mg/ml LarE-C176A (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate ...Details: 5 ul 8 mg/ml LarE-C176A (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→48.67 Å / Num. obs: 82741 / % possible obs: 99.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 41.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Net I/σ(I): 18.9 / Num. measured all: 932078 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.3911.21.1343450.7020.3471.18397.3
12.19-48.678.10.0237080.9990.0080.02597.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.61 Å48.67 Å
Translation7.61 Å48.67 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASER2.7.16phasing
PHENIX1.12-2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDQ
Resolution: 2.35→48.67 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.2436 7813 5 %
Rwork0.1872 --
obs0.19 78172 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.55 Å2 / Biso mean: 56.3395 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.35→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11365 0 55 493 11913
Biso mean--52.18 48.37 -
Num. residues----1500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711585
X-RAY DIFFRACTIONf_angle_d0.92215729
X-RAY DIFFRACTIONf_chiral_restr0.0591843
X-RAY DIFFRACTIONf_plane_restr0.0062035
X-RAY DIFFRACTIONf_dihedral_angle_d4.1026859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6043X-RAY DIFFRACTION10.225TORSIONAL
12B6043X-RAY DIFFRACTION10.225TORSIONAL
13C6043X-RAY DIFFRACTION10.225TORSIONAL
14D6043X-RAY DIFFRACTION10.225TORSIONAL
15E6043X-RAY DIFFRACTION10.225TORSIONAL
16F6043X-RAY DIFFRACTION10.225TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3466-2.37330.3362220.29244781500395
2.3733-2.40120.3442450.26784989523499
2.4012-2.43050.30312670.2644903517099
2.4305-2.46130.33952870.26644914520199
2.4613-2.49370.33662750.28264920519599
2.4937-2.52780.33752540.26835014526899
2.5278-2.56390.33042470.25284895514299
2.5639-2.60220.31522600.24854986524699
2.6022-2.64290.30022560.23614971522799
2.6429-2.68620.31782610.23164894515599
2.6862-2.73250.27072320.234978521099
2.7325-2.78220.30932630.22654966522999
2.7822-2.83570.25542600.223549665226100
2.8357-2.89360.27692630.214949355198100
2.8936-2.95650.28222820.220549555237100
2.9565-3.02520.32512650.231949825247100
3.0252-3.10090.30412870.225549035190100
3.1009-3.18470.30472290.220249915220100
3.1847-3.27840.26472670.204549575224100
3.2784-3.38420.27042550.200649785233100
3.3842-3.50510.25832470.184349775224100
3.5051-3.64540.21782700.176349435213100
3.6454-3.81130.22942820.16549245206100
3.8113-4.01210.18872470.152350035250100
4.0121-4.26330.20832460.147950035249100
4.2633-4.59230.18282410.13549745215100
4.5923-5.0540.20472780.135649645242100
5.054-5.78430.17832750.149249605235100
5.7843-7.28370.20612970.169749525249100
7.2837-48.6840.20212530.1664952520599
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)
16.70454.87590.91357.61550.30452.9041-0.05070.21440.157-0.08570.18630.1458-0.0140.2431-0.15080.34130.0693-0.0440.40340.00380.244618.97830.2741-14.3094
22.8698-3.01581.2232.2764-5.3953.92080.41790.4655-0.2121-1.8221-0.7358-0.34351.23681.09680.24150.70390.2519-0.02570.72020.02440.398518.1865-16.221-25.6837
39.9189-1.93513.72286.9883-2.59067.95180.26821.2152-0.5494-0.43050.0771-0.64580.64342.1854-0.35650.3699-0.0080.01060.7293-0.07980.439229.8318-0.3801-15.3048
40.4339-0.4086-0.73564.3496-0.57410.05320.04430.11-0.0639-0.6333-0.1360.2494-0.1211-0.1270.08870.5890.1643-0.13640.46080.00870.367917.1303-21.5325-8.6772
55.0592-1.93870.16332.14280.01632.37350.18550.32140.4223-0.2454-0.1176-0.1714-0.24090.0465-0.06310.44430.0697-0.03540.29530.02860.365724.3859-32.6371-1.6398
61.18270.3371-0.2361.8915-2.58234.47270.00010.00980.20770.1459-0.1542-0.0168-0.34450.20460.13420.25470.014-0.06770.1979-0.04850.32858.92381.976423.032
76.26827.5639-4.0639.349-6.29696.1786-0.18930.35110.52630.08120.39620.7354-0.1103-0.4962-0.15840.30640.0832-0.10130.3275-0.06010.34-1.49320.067129.2981
83.0056-2.8532-5.6055.66863.22867.6359-0.35020.456-0.63950.1584-0.16470.50830.731-0.70760.5040.3187-0.0152-0.07040.37070.01330.38494.86560.691112.1305
9-0.3981-0.22740.33151.5793-0.9981.22770.0310.07960.0968-0.3643-0.06320.06110.2231-0.12520.04120.3522-0.0061-0.04830.2819-0.01420.296712.869-15.153629.1874
103.1971-0.83350.08285.99832.56062.6669-0.0527-0.0881-0.0325-0.171-0.0013-0.0378-0.06570.11340.11250.25820.0041-0.00720.25930.00840.214318.3889-27.038627.5268
117.41652.1137-2.42488.76123.05539.018-0.48430.15760.0601-0.0971-0.2988-0.1858-0.0235-0.24760.7590.27030.0576-0.05960.1614-0.01860.35613.4167-29.590228.9395
125.7463-4.0481-0.2646.1179-0.76272.16520.1386-0.1609-0.2318-0.09370.11620.1637-0.0620.0835-0.24230.3163-0.0576-0.06080.24950.0240.367444.16644.752310.9521
138.4273-6.32446.93132.07011.67061.9346-0.23-0.61880.41550.61680.0696-0.9896-0.4632-0.57770.3790.3667-0.03450.01560.441-0.10370.520655.02714.258314.965
146.2053-3.3265-2.35635.10832.77863.6657-0.5675-1.4931-0.15320.49050.3801-0.26240.11850.46430.15740.4261-0.05070.01090.51980.04920.426644.135910.510720.9983
152.19820.76072.58360.49890.26151.7263-0.1324-0.6492-0.4205-0.18820.39011.41730.5085-0.4104-0.23950.4958-0.0203-0.00860.5420.29050.859531.40351.714215.0456
163.04670.99920.40853.38090.871.7579-0.02-0.07660.1901-0.11130.0536-0.2621-0.16460.0132-0.04080.39370.07190.01240.27580.03820.308645.9637-23.801513.9402
178.40222.5108-2.05543.7839-4.07174.25970.0037-0.05140.8893-0.01250.20190.327-0.00180.0801-0.29610.34320.0499-0.02970.2606-0.02450.261146.0876-28.398318.3048
186.6355-4.95741.20774.8090.71492.5224-0.8227-1.29290.35170.91521.4325-0.98160.11220.3457-0.5351.64750.18510.46850.6887-0.00021.17720.7603-77.834835.2743
190.60751.52280.74424.2912.20251.21070.1996-0.5434-1.0127-1.1569-1.00250.36211.3563-0.60390.64451.3263-0.04410.37730.36160.07791.12528.0404-70.481131.9963
202.9266-1.7555-0.41795.63491.58651.10410.00440.2697-0.8245-2.129-0.60780.25191.05310.15010.51152.0728-0.10220.20050.54780.03650.82389.0087-70.731326.3124
212.0531-2.7263-0.98538.2192-0.71921.2538-0.4251-1.1154-0.47790.33110.35240.32140.3225-0.01670.07670.647-0.13220.16980.7134-0.00440.55991.5708-54.22642.8307
224.6262-2.12860.66178.10916.98647.7540.0607-1.392-0.54291.6927-0.13150.70571.55690.1950.1280.875-0.08570.15970.67210.12810.53076.0768-66.987343.5946
231.2706-1.645-0.1785.77974.88045.83471.1519-0.55560.9415-0.1050.0213-0.2627-0.53331.309-1.19371.52560.25650.35891.20010.21060.714220.4333-73.498541.4437
242.5402-2.7172-2.27872.21512.25041.80350.966-0.34240.5652-1.67440.0347-1.375-0.71921.0496-0.91381.13620.08250.3040.8764-0.12051.151724.6788-68.407427.4143
252.42361.36820.28983.19930.45234.45910.0775-0.0225-0.34260.0545-0.13280.07750.5843-0.14180.05960.44850.0295-0.00780.2096-0.05150.374210.4216-44.176425.7821
264.91284.36940.57628.00974.86019.9453-0.5874-0.3521-0.30790.3560.04380.11770.5492-0.30980.44070.3423-0.02470.08970.2512-0.00630.225811.6628-38.362327.609
271.07312.04440.64769.50593.38232.67190.0396-0.0971-0.47420.79930.0243-0.6470.92250.2813-0.06020.67810.146-0.00690.46140.010.514952.5789-64.939525.4631
283.4597-0.50180.38834.1599-0.65755.3107-0.02470.1946-0.0551-0.32130.069-0.19180.14930.2079-0.05270.29090.0389-0.02080.26750.03820.24844.2348-39.439422.4114
290.69250.2054-0.40724.9942-1.99372.7538-0.02750.13-0.2421-0.3506-0.09720.26590.1418-0.08050.11680.50430.0164-0.02280.3051-0.04490.592925.2097-76.4889-3.3577
306.6683-0.9691-3.16127.06055.2498.62710.07470.64990.769-0.236-0.61171.4966-0.8943-1.25810.49270.5510.03660.01520.33460.050.963915.7987-79.57013.7849
310.3457-0.60940.45926.0838-4.87983.7070.2185-0.0284-0.261-0.09820.14570.67650.11730.0197-0.37620.55130.0337-0.12150.3078-0.01740.426324.4107-62.1437-1.2686
325.1093-1.3739-0.09474.55921.21412.428-0.0941-0.0529-0.2656-0.16730.04980.20580.3820.03160.05650.41710.0416-0.0430.21330.05190.252129.3162-46.0574-1.0536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 80 )A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 115 )A81 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 164 )A116 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 206 )A165 - 206
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 276 )A207 - 276
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 95 )B2 - 95
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 115 )B96 - 115
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 164 )B116 - 164
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 206 )B165 - 206
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 245 )B207 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid 246 through 259 )B246 - 259
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 95 )C2 - 95
13X-RAY DIFFRACTION13chain 'C' and (resid 96 through 115 )C96 - 115
14X-RAY DIFFRACTION14chain 'C' and (resid 116 through 154 )C116 - 154
15X-RAY DIFFRACTION15chain 'C' and (resid 155 through 177 )C155 - 177
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 245 )C178 - 245
17X-RAY DIFFRACTION17chain 'C' and (resid 246 through 259 )C246 - 259
18X-RAY DIFFRACTION18chain 'D' and (resid 5 through 42 )D5 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 58 )D43 - 58
20X-RAY DIFFRACTION20chain 'D' and (resid 59 through 80 )D59 - 80
21X-RAY DIFFRACTION21chain 'D' and (resid 81 through 95 )D81 - 95
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 115 )D96 - 115
23X-RAY DIFFRACTION23chain 'D' and (resid 116 through 154 )D116 - 154
24X-RAY DIFFRACTION24chain 'D' and (resid 155 through 177 )D155 - 177
25X-RAY DIFFRACTION25chain 'D' and (resid 178 through 245 )D178 - 245
26X-RAY DIFFRACTION26chain 'D' and (resid 246 through 259 )D246 - 259
27X-RAY DIFFRACTION27chain 'E' and (resid 2 through 189 )E2 - 189
28X-RAY DIFFRACTION28chain 'E' and (resid 190 through 279 )E190 - 279
29X-RAY DIFFRACTION29chain 'F' and (resid 2 through 115 )F2 - 115
30X-RAY DIFFRACTION30chain 'F' and (resid 116 through 164 )F116 - 164
31X-RAY DIFFRACTION31chain 'F' and (resid 165 through 189 )F165 - 189
32X-RAY DIFFRACTION32chain 'F' and (resid 190 through 260 )F190 - 260

+
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