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- PDB-3zzn: 5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 3zzn
Title5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus thermophillus
ComponentsLACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PROTEIN ADAPTATION / CONFORMATIONAL ENERGY LANDSCAPE / HYPERTHERMOPHILIC
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsColletier, J.P. / Mraihi, S. / Madern, D.
CitationJournal: Mol. Biol. Evol. / Year: 2012
Title: Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions.
Authors: Colletier, J.P. / Aleksandrov, A. / Coquelle, N. / Mraihi, S. / Mendoza-Barbera, E. / Field, M. / Madern, D.
History
DepositionSep 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2May 30, 2012Group: Other
Revision 1.3Feb 28, 2018Group: Advisory / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_validate_polymer_linkage
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Dec 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 / 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 / _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: LACTATE DEHYDROGENASE
B: LACTATE DEHYDROGENASE
C: LACTATE DEHYDROGENASE
D: LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2526
Polymers130,3974
Non-polymers8542
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-76.9 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.123, 59.597, 153.076
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 22:80 OR RESSEQ 83:103 OR RESSEQ...
211CHAIN D AND (RESSEQ 22:80 OR RESSEQ 83:103 OR RESSEQ...
112CHAIN B AND (RESSEQ 22:80 OR RESSEQ 83:103 OR RESSEQ...
212CHAIN C AND (RESSEQ 22:80 OR RESSEQ 83:103 OR RESSEQ...

NCS ensembles :
ID
1
2

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Components

#1: Protein
LACTATE DEHYDROGENASE


Mass: 32599.373 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 58 TO TRP ENGINEERED RESIDUE IN CHAIN A, ARG 128 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 58 TO TRP ENGINEERED RESIDUE IN CHAIN A, ARG 128 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 260 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 292 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 58 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 128 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 260 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 292 TO ALA ENGINEERED RESIDUE IN CHAIN C, ARG 58 TO TRP ENGINEERED RESIDUE IN CHAIN C, ARG 128 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 260 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 292 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 58 TO TRP ENGINEERED RESIDUE IN CHAIN D, ARG 128 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 260 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 292 TO ALA

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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: 2.76 Å3/Da / Density % sol: 55.43 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 5-MUT TT-LDH WAS CRYSTALLIZED AT 10MG/ML BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD, FOLLOWING THE MIXING OF THE PROTEIN AND THE MOTHER-LIQUOR SOLUTIONS AT A 1:1 RATIO. THE MOTHER LIQUOR ...Details: 5-MUT TT-LDH WAS CRYSTALLIZED AT 10MG/ML BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD, FOLLOWING THE MIXING OF THE PROTEIN AND THE MOTHER-LIQUOR SOLUTIONS AT A 1:1 RATIO. THE MOTHER LIQUOR SOLUTION WAS 0.1 M HEPES BUFFER PH 9, 18-20% PEG 6000, 2 M LICL2, 500 MICROMOLAR ADP. CRYSTALS GREW WITHIN A WEEK AT 4 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→45.53 Å / Num. obs: 30826 / % possible obs: 96.8 % / Observed criterion σ(I): 3 / Redundancy: 3.47 % / Biso Wilson estimate: 41.99 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.25
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.05 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6M
Resolution: 2.9→45.47 Å / SU ML: 0.87 / σ(F): 1.99 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 2039 6.6 %
Rwork0.1878 --
obs0.1919 30812 96.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.828 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2486 Å20 Å2-3.2788 Å2
2--1.8068 Å20 Å2
3----1.5582 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9135 0 54 416 9605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159658
X-RAY DIFFRACTIONf_angle_d1.70413200
X-RAY DIFFRACTIONf_dihedral_angle_d18.0573492
X-RAY DIFFRACTIONf_chiral_restr0.1071526
X-RAY DIFFRACTIONf_plane_restr0.0161731
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2175X-RAY DIFFRACTIONPOSITIONAL
12D2175X-RAY DIFFRACTIONPOSITIONAL0.468
21B2241X-RAY DIFFRACTIONPOSITIONAL
22C2241X-RAY DIFFRACTIONPOSITIONAL0.601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.96750.33881430.27681887X-RAY DIFFRACTION97
2.9675-3.04170.34941420.26431883X-RAY DIFFRACTION97
3.0417-3.12390.30781390.26941934X-RAY DIFFRACTION97
3.1239-3.21580.38541450.25861864X-RAY DIFFRACTION97
3.2158-3.31950.30261480.2261909X-RAY DIFFRACTION98
3.3195-3.43820.32321410.20191906X-RAY DIFFRACTION98
3.4382-3.57580.25431440.19711913X-RAY DIFFRACTION97
3.5758-3.73840.27731580.18881914X-RAY DIFFRACTION97
3.7384-3.93540.25861500.1811889X-RAY DIFFRACTION97
3.9354-4.18180.24171560.17281881X-RAY DIFFRACTION97
4.1818-4.50440.18911480.15251906X-RAY DIFFRACTION97
4.5044-4.95720.17321050.13821965X-RAY DIFFRACTION95
4.9572-5.67340.20371040.16161942X-RAY DIFFRACTION97
5.6734-7.14340.24191050.16451981X-RAY DIFFRACTION97
7.1434-45.47560.15011110.16541999X-RAY DIFFRACTION94
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)
10.6325-0.038-0.15980.55620.4750.42270.0050.05980.1487-0.0789-0.01860.0132-0.1068-0.035-0.02630.07250.0063-0.00380.04480.04680.079132.9735-10.927358.4254
20.4373-0.06780.03650.58130.26360.62640.0528-0.0156-0.0848-0.0247-0.02470.1250.043-0.11580.0560.0542-0.02740.005-0.1470.01370.076326.9841-30.417352.0686
30.681-0.77580.2531.225-0.31080.10130.1720.1225-0.1048-0.1981-0.05680.23040.0764-0.00550.34250.06270.0498-0.0470.0775-0.10440.248428.8013-36.191847.5731
40.5583-0.1586-0.12790.54370.16020.823-0.0589-0.10230.06450.0351-0.00290.0237-0.00370.0597-0.16130.0910.07130.01210.113-0.06540.048842.4458-39.181660.9082
51.13430.21770.00220.30210.04950.68620.04860.01830.05210.0221-0.031-0.0006-0.12230.12150.021-0.0275-0.01910.00490.07720.04280.178850.7435-19.526450.1762
64.4812-2.05142.25412.6402-0.7344.48830.22820.42280.6833-0.1934-0.3684-0.4187-0.25140.44240.25670.12010.0041-0.00110.2540.08960.294460.2628-13.351549.1354
71.04650.577-0.87381.8018-1.62123.1640.0932-0.24020.09470.2736-0.3375-0.3253-0.50910.55130.20470.1962-0.0517-0.10840.15910.03620.238651.0947-12.080460.8928
80.5719-0.0483-0.07040.4260.08710.49010.04060.0721-0.1188-0.005-0.0473-0.25150.11030.2715-0.0229-0.15620.15660.11020.0684-0.07580.066150.5137-29.697846.9655
92.33032.0794-1.20412.3356-1.17530.94280.0653-0.2197-0.11780.002-0.2333-0.52070.07280.38050.26910.05370.0636-0.06720.26710.01630.355961.0217-33.084560.8344
100.15960.0144-0.01090.63660.05220.3035-0.02560.1021-0.1031-0.2128-0.1117-0.07610.13520.008-0.12160.37940.24270.2509-0.163-0.1774-0.109435.2681-20.410418.0412
111.17020.08610.39290.92010.61611.0013-0.10880.28570.0701-0.3355-0.18430.0016-0.0761-0.1553-0.25670.5604-0.06670.1679-0.00210.09-0.034823.6175-25.95359.9303
120.6997-0.307-0.14061.26350.63911.9939-0.07370.1365-0.0188-0.2569-0.02020.0970.0566-0.36370.07020.35330.018-0.10110.2622-0.0471-0.050311.4608-13.884725.1492
132.87461.17562.47051.35130.80452.8610.093-0.14190.1981-0.2971-0.29650.2306-0.159-0.6249-0.42280.37860.2442-0.13120.57550.02460.30971.6102-8.648229.3368
141.2566-0.4987-0.96272.2966-0.08231.3001-0.21030.3489-0.3258-0.4522-0.0430.30620.2985-0.42280.0610.3072-0.0547-0.01180.2694-0.03420.115511.4826-23.715622.7125
152.5381-0.1227-1.06372.25162.01652.6104-0.01280.63250.0067-0.6706-0.07270.2905-0.0841-0.56050.55790.5999-0.0208-0.29470.7398-0.05620.28430.6335-19.11969.9452
160.8446-0.5256-0.77840.47640.65770.93720.06860.0160.1724-0.11730.0406-0.0763-0.140.02870.52840.1860.0217-0.19860.02720.05220.170931.4818-3.220756.8123
172.5282-0.02180.18051.5338-0.14030.83870.0035-0.128-0.14690.1259-0.01320.0984-0.0725-0.2038-0.12080.05490.0822-0.00330.1278-0.01390.083716.2385-6.46368.1471
180.3805-0.13510.02040.1592-0.00480.0965-0.0824-0.0432-0.1247-0.0325-0.00050.07150.0144-0.11870.0558-0.17510.1876-0.11320.1375-0.05430.10659.9369-18.2148.1375
194.1035-1.0517-0.78782.04910.7652.44480.020.5171-0.3365-0.1752-0.16480.41970.0299-0.30540.03810.09090.0528-0.05160.2928-0.02520.31310.6004-23.00842.7957
202.73980.12660.95772.2274-0.38712.84030.02450.2687-0.4498-0.21910.0210.35490.4382-0.4266-0.19760.1258-0.06870.05180.1091-0.07010.26047.9636-30.219552.6483
210.9429-0.45410.22850.5892-0.20570.1501-0.1153-0.02690.0684-0.0177-0.08190.1988-0.2348-0.3423-0.3453-0.42440.4623-0.1638-0.07690.05190.095210.1764-7.834750.5918
220.84330.12390.33990.58650.41890.812-0.09-0.42450.07930.1504-0.07730.2248-0.1057-0.41030.64320.12160.13890.05660.4872-0.07920.2064-1.7454-11.370663.0097
233.7197-1.2885-2.34352.17620.11075.57780.3560.27370.2425-0.3002-0.04220.18-0.8673-1.0357-0.19780.60710.1267-0.09840.33460.00550.249810.599-1.678319.9374
241.75860.6861-0.27460.63380.19140.29160.2642-0.15520.11620.1747-0.10480.0766-0.2922-0.11220.0110.57730.13920.04450.2196-0.02970.124830.11594.660728.0598
250.5010.22-0.0051.4947-0.5941.0119-0.09180.1398-0.0593-0.28190.0352-0.12590.0140.0621-0.05290.4823-0.00840.11170.0058-0.05960.070945.50987.745216.6471
260.3642-0.0044-0.25021.3138-0.49820.8184-0.01780.04920.1289-0.1681-0.0663-0.1587-0.03980.0929-0.13950.29940.09330.3180.0070.30530.004152.0297-12.161228.0586
270.41440.3537-0.10981.0730.37870.3106-0.05790.06250.0988-0.2779-0.00670.0132-0.311-0.0523-0.04610.56250.06660.01860.05540.07980.008428.6546-1.190323.0391
285.15340.58770.30212.7801-3.25737.00890.4082-0.166-0.4137-0.4212-0.3035-0.31610.35780.72850.77920.24260.1420.19140.33630.06610.438661.5354-18.78630.2706
292.2881-0.31720.91170.1959-0.70573.67820.07330.0846-0.3514-0.2208-0.1499-0.15080.80060.64330.75780.76360.17580.41420.22730.00950.301453.5834-19.726917.7674
301.59750.10120.57232.0057-0.02453.21980.0581-0.00380.2232-0.1473-0.1978-0.5161-0.5040.4666-0.06260.2607-0.02240.11750.14290.00480.256751.8133-1.803931.1778
314.4503-3.30491.98923.1049-1.26781.71680.110.53640.1539-0.4467-0.4001-0.7336-0.28070.88060.30390.4855-0.17770.30120.71590.1020.594663.7660.978818.7357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 22:72)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 22:72)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 73:96)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 97:153)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 154:196)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 197:214)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 215:247)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 248:308)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 309:331)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 22:72)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 73:153)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 154:196)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 197:214)
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 248:308)
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 309:331)
16X-RAY DIFFRACTION16CHAIN A AND (RESSEQ 73:96)
17X-RAY DIFFRACTION17CHAIN A AND (RESSEQ 97:153)
18X-RAY DIFFRACTION18CHAIN A AND (RESSEQ 154:196)
19X-RAY DIFFRACTION19CHAIN A AND (RESSEQ 197:214)
20X-RAY DIFFRACTION20CHAIN A AND (RESSEQ 215:247)
21X-RAY DIFFRACTION21CHAIN A AND (RESSEQ 248:308)
22X-RAY DIFFRACTION22CHAIN A AND (RESSEQ 309:331)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 215:247)
24X-RAY DIFFRACTION24CHAIN C AND (RESSEQ 73:96)
25X-RAY DIFFRACTION25CHAIN C AND (RESSEQ 97:153)
26X-RAY DIFFRACTION26CHAIN C AND (RESSEQ 154:196)
27X-RAY DIFFRACTION27CHAIN C AND (RESSEQ 22:72)
28X-RAY DIFFRACTION28CHAIN C AND (RESSEQ 197:214)
29X-RAY DIFFRACTION29CHAIN C AND (RESSEQ 215:247)
30X-RAY DIFFRACTION30CHAIN C AND (RESSEQ 248:308)
31X-RAY DIFFRACTION31CHAIN C AND (RESSEQ 309:331)

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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

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