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- PDB-8j4y: Structure of Mycobacterium tuberculosis NrdF2:NrdIcomplex (reduce... -

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Basic information

Entry
Database: PDB / ID: 8j4y
TitleStructure of Mycobacterium tuberculosis NrdF2:NrdIcomplex (reduced) determined at 3 angstrom resolution
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductase subunit beta nrdF2
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase NrdF2 / NrdI protein complex / Metal cofactor assembly
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / DNA replication / metal ion binding
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like ...Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Flavoprotein-like superfamily / Ferritin-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / HYDROXIDE ION / PEROXIDE ION / Ribonucleoside-diphosphate reductase subunit beta nrdF2 / Protein NrdI
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsYadav, L.R. / Mande, S.C.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-Centre of Excellence Grant (BT/PR15450/COE/34/46/2016). India
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria.
Authors: Yadav, L.R. / Sharma, V. / Shanmugam, M. / Mande, S.C.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta nrdF2
B: Ribonucleoside-diphosphate reductase subunit beta nrdF2
C: Ribonucleoside-diphosphate reductase subunit beta nrdF2
D: Ribonucleoside-diphosphate reductase subunit beta nrdF2
E: Ribonucleoside-diphosphate reductase subunit beta nrdF2
F: Ribonucleoside-diphosphate reductase subunit beta nrdF2
G: Protein NrdI
I: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,71929
Polymers254,9838
Non-polymers1,73621
Water28816
1
A: Ribonucleoside-diphosphate reductase subunit beta nrdF2
C: Ribonucleoside-diphosphate reductase subunit beta nrdF2
G: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,22210
Polymers90,4973
Non-polymers7257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-50 kcal/mol
Surface area26610 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase subunit beta nrdF2
hetero molecules

B: Ribonucleoside-diphosphate reductase subunit beta nrdF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2428
Polymers73,9892
Non-polymers2546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area4140 Å2
ΔGint-43 kcal/mol
Surface area22200 Å2
MethodPISA
3
D: Ribonucleoside-diphosphate reductase subunit beta nrdF2
F: Ribonucleoside-diphosphate reductase subunit beta nrdF2
I: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,27112
Polymers90,4973
Non-polymers7749
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-39 kcal/mol
Surface area26420 Å2
MethodPISA
4
E: Ribonucleoside-diphosphate reductase subunit beta nrdF2
hetero molecules

E: Ribonucleoside-diphosphate reductase subunit beta nrdF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2086
Polymers73,9892
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.430, 160.430, 310.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 11 through 301)
d_2ens_1(chain "B" and (resid 11 through 292 or resid 301))
d_3ens_1(chain "C" and resid 11 through 301)
d_4ens_1(chain "D" and resid 11 through 301)
d_5ens_1(chain "E" and resid 11 through 301)
d_6ens_1(chain "F" and (resid 11 through 292 or resid 302))
d_1ens_2chain "G"
d_2ens_2(chain "I" and (resid 7 through 55 or resid 62 through 141))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALSERSERAA11 - 29211 - 292
d_21ens_1VALVALSERSERBB11 - 29211 - 292
d_31ens_1VALVALSERSERCC11 - 29211 - 292
d_41ens_1VALVALSERSERDD11 - 29211 - 292
d_51ens_1VALVALSERSEREE11 - 29211 - 292
d_61ens_1VALVALSERSERFF11 - 29211 - 292
d_11ens_2SERSERTHRTHRGG7 - 1417 - 141
d_21ens_2SERSERARGARGIH7 - 557 - 55
d_22ens_2ALAALATHRTHRIH62 - 14162 - 141

NCS ensembles :
ID
ens_1
ens_2

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Components

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Protein , 2 types, 8 molecules ABCDEFGI

#1: Protein
Ribonucleoside-diphosphate reductase subunit beta nrdF2 / Ribonucleoside-diphosphate reductase nrdF2 / Ribonucleotide reductase R2-2 small subunit


Mass: 36994.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Ribonucleotide reductase NrdF2 metallocofactor subunit essential for the initiation of nucleotide reduction
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: nrdF2 / Plasmid: pET32a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WH71, ribonucleoside-diphosphate reductase
#2: Protein Protein NrdI


Mass: 16508.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ribonucleotide reductase NrdI subunit essential for meta cofactor assembly
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: nrdI / Plasmid: pET32a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WIZ3

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Non-polymers , 5 types, 37 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6, 1.4M NaCl, 0.075M sodium phosphate monobasic, 0.075M potassium phosphate monobasic
Temp details: 293.15

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.02→91.58 Å / Num. obs: 80104 / % possible obs: 99.9 % / Redundancy: 47.1 % / Biso Wilson estimate: 53.01 Å2 / CC1/2: 0.912 / CC star: 0.977 / Net I/σ(I): 9.7
Reflection shellResolution: 3.02→3.128 Å / Redundancy: 46.8 % / Num. unique obs: 7862 / CC1/2: 0.39 / CC star: 0.749 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→91.58 Å / SU ML: 0.4525 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 4028 5.03 %
Rwork0.2296 75984 -
obs0.2314 80012 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.23 Å2
Refinement stepCycle: LAST / Resolution: 3.02→91.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15852 0 84 16 15952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002516276
X-RAY DIFFRACTIONf_angle_d0.425822117
X-RAY DIFFRACTIONf_chiral_restr0.03472448
X-RAY DIFFRACTIONf_plane_restr0.00392829
X-RAY DIFFRACTIONf_dihedral_angle_d6.31442191
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.760391535222
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.899872578738
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.716306652281
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.768270112513
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.81134109084
ens_2d_2GGX-RAY DIFFRACTIONTorsion NCS0.96001983134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.060.37421540.35172527X-RAY DIFFRACTION99.96
3.06-3.090.36741580.34022585X-RAY DIFFRACTION99.96
3.09-3.130.36341370.33682548X-RAY DIFFRACTION99.96
3.13-3.170.3681360.32782585X-RAY DIFFRACTION100
3.17-3.220.41621390.32062589X-RAY DIFFRACTION100
3.22-3.260.30151540.30872582X-RAY DIFFRACTION100
3.26-3.310.31441200.29642569X-RAY DIFFRACTION100
3.31-3.360.32291090.28822634X-RAY DIFFRACTION100
3.36-3.420.31081220.29362613X-RAY DIFFRACTION100
3.42-3.480.31621270.2792606X-RAY DIFFRACTION100
3.48-3.540.3131350.27272596X-RAY DIFFRACTION100
3.54-3.610.32431450.25782560X-RAY DIFFRACTION100
3.61-3.680.29571190.25232618X-RAY DIFFRACTION99.96
3.68-3.760.22641430.23372607X-RAY DIFFRACTION99.96
3.76-3.850.27611570.23572589X-RAY DIFFRACTION100
3.85-3.950.28151420.23062590X-RAY DIFFRACTION100
3.95-4.050.28631280.21232634X-RAY DIFFRACTION99.96
4.05-4.170.24761330.20812611X-RAY DIFFRACTION100
4.17-4.310.25291460.21532593X-RAY DIFFRACTION99.96
4.31-4.460.26551610.20892619X-RAY DIFFRACTION100
4.46-4.640.2291390.20112593X-RAY DIFFRACTION100
4.64-4.850.21221400.18612666X-RAY DIFFRACTION100
4.85-5.110.1981270.18282618X-RAY DIFFRACTION100
5.11-5.430.26661470.20022659X-RAY DIFFRACTION100
5.43-5.840.22661400.20632654X-RAY DIFFRACTION99.93
5.84-6.430.22461270.19082696X-RAY DIFFRACTION100
6.43-7.360.21421380.17892683X-RAY DIFFRACTION99.93
7.36-9.270.20891510.16372724X-RAY DIFFRACTION100
9.28-91.580.20841540.18422836X-RAY DIFFRACTION97.49
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)
13.983617201090.770616657449-2.683027633610.872753038817-0.4546773423084.84435576622-0.155250897723-0.6803325228870.7191634101380.1282079714280.1944491740890.335185779359-0.650273250258-0.673198596223-0.1067837126510.9079794937960.262600863674-0.1876442947310.695165147553-0.2473454350990.472924104627-32.957-51.73-21.492
21.19349940727-0.07716571895230.600087179860.2978828318340.3143583179051.08775777068-0.377246649511-0.7306655987660.2737492438380.292566902680.120964805507-0.0383454696052-0.183564517078-0.592715746620.1229255228850.7391283714590.2591948581730.04141904880950.651799400913-0.1964428924820.517458836191-44.314-59.923-28.416
33.51407059564-0.798331555297-1.924366609193.804215270061.914152248933.20743264562-0.02571481501990.09882287051260.199437609115-0.544513788122-0.110431632301-0.00993806734284-0.0549881598752-0.2312772265210.04456157833070.5800715787580.0481374856511-0.03159104559020.0998811156314-0.0003788780506190.574439326441-82.505-71.086-60.83
42.41222301177-0.0452158278660.5994789080861.05936325550.6152998565130.603857568407-0.262169070007-0.5002515967980.208209583038-0.2773881740380.320361011349-0.170911308968-0.2961530882750.127502627227-0.04466555202980.5826512508620.03923850361630.07010116811780.093451821949-0.09636618072080.510834534241-61.85-74.641-54.153
58.337904305973.77883510095-1.767921568393.19695125977-1.34653221771.618968274650.00189122195799-0.4978281296280.872867606450.255014438751-0.01978737453580.519969491542-0.492882737858-0.2695764748580.06485170280571.019381234560.226696088675-0.1562702493720.496379231365-0.1253542405840.344223935351-16.738-55.392-16.511
62.674651088880.09507004926740.8102255694162.267995727380.7638594338280.932792250183-0.201221803527-0.3287255800840.1783697112360.392278622790.0597690423061-0.0677616353895-0.275461773745-0.05126842785050.1248873880320.7364121787790.0974770488228-0.04484455508370.453961331867-0.05483164497490.280761112592-8.603-65.286-17.07
70.860498062382-0.237602265695-0.365986857323.8827072624-1.890276897161.817236625530.0484328442149-0.1381458123740.122452333188-0.132992565043-0.176740317479-0.1048506716820.220578675775-0.14356529160.1234959294350.3777589687730.02314604340670.07119169323860.1331558740330.02878838180220.408159253616-20.125-42.187-74.899
81.34549100556-0.6699334624331.29601044592.79822378227-1.500661759663.477968385140.0279603331091-0.2557676232790.456418799450.7276943523580.00736409711363-0.0373108786341-0.193110321311-0.3296342322090.04340990324130.5440002236120.03751342193910.1996743843040.244357253997-0.007677632336730.602555517897-23.269-33.648-63.512
92.92899649403-1.10872319454-0.2021763155384.24140650302-0.8802553299340.7597294069970.290368825235-0.470094073517-0.06319594570121.69751812939-0.316177944710.1477609931110.142397307218-0.0268700424796-0.07437807282331.55080087024-0.4036248155-0.09650746518950.688493866737-0.01304931139470.663061047951-2.64-9.211-33.421
102.108511739990.690360253978-0.04016824034953.20274502915-0.2015774564551.39080326920.405211475884-0.323586690655-0.165119703421.12503642227-0.4227676047910.1680200534140.02921893242550.139494674273-0.0009127069872311.27924046894-0.1640151219110.02771216669090.4135783209670.01184785237690.73325818961-6.808-17.477-43.243
116.991825002454.11421684518-2.50297325175.83286551709-1.904046121974.53358296455-0.1353603959690.295870790005-0.340838809226-0.2235238131620.156687200849-0.4489147660760.224725361906-0.0189036234837-0.0056430982670.3742630681130.0878388178162-0.06002135229180.0832437000850.06296952056030.436610446398-19.327-51.713-84.265
122.16492065120.804904422316-0.5789602495492.02767023118-0.3088663573090.9143233932450.179487956759-0.0184135179048-0.3940219068360.0195167422253-0.184977943384-0.2660028174730.149597242970.04590802252250.01969381732360.4147937082080.0191063369752-0.0452952103510.15820202110.01383422847320.477740837864-16.757-72.508-78.449
131.829163448320.0655412630104-0.349036371232.341494697190.02262518315220.118136730454-0.155393726951-0.4964054990990.0755054151620.1414633945020.3541843334810.0635095673109-0.369884549716-0.39654536552-0.2120022115420.9109579891330.235756008096-0.03101663666191.25861925084-0.1023096541890.348266117821-14.897-64.9610.893
147.241169588881.68684340071.815134635976.732761236890.4840186229268.78388845473-0.3243888127661.038943497960.17191685371-1.238972135260.2751106344770.0958562053850.3060726875150.1756519804310.01986073858210.6366196161140.01230821131310.02528810870650.510500464651-0.06060458939510.539274252341-15.944-65.51-106.941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:57 )A10 - 57
2X-RAY DIFFRACTION2( CHAIN A AND RESID 58:292 )A58 - 292
3X-RAY DIFFRACTION3( CHAIN B AND RESID 10:42 )B10 - 42
4X-RAY DIFFRACTION4( CHAIN B AND RESID 43:293 )B43 - 293
5X-RAY DIFFRACTION5( CHAIN C AND RESID 10:71 )C10 - 71
6X-RAY DIFFRACTION6( CHAIN C AND RESID 72:292 )C72 - 292
7X-RAY DIFFRACTION7( CHAIN D AND RESID 11:149 )D11 - 149
8X-RAY DIFFRACTION8( CHAIN D AND RESID 150:292 )D150 - 292
9X-RAY DIFFRACTION9( CHAIN E AND RESID 10:65 )E10 - 65
10X-RAY DIFFRACTION10( CHAIN E AND RESID 66:292 )E66 - 292
11X-RAY DIFFRACTION11( CHAIN F AND RESID 9:43 )F9 - 43
12X-RAY DIFFRACTION12( CHAIN F AND RESID 44:293 )F44 - 293
13X-RAY DIFFRACTION13( CHAIN G AND RESID 7:140 )G7 - 140
14X-RAY DIFFRACTION14( CHAIN I AND RESID 7:141 )I7 - 141

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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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