[English] 日本語
Yorodumi
- PDB-29um: Mo-Nitrogenase, MoFe protein, P2+ redox state, -150 mV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 29um
TitleMo-Nitrogenase, MoFe protein, P2+ redox state, -150 mV
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Mo-Nitrogenase / MoFe protein / P2+ redox state / -150 mV
Function / homology
Function and homology information


nitrogen fixation / molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER, OXIDIZED / ACETATE ION / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLaxmi, S. / Seefeldt, L.C. / Carr, S.B. / Vincent, K.A.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
Department of Energy (DOE, United States)DE-SC0010687 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Structural Characterization of Four Redox States of the P-cluster in Molybdenum Nitrogenase via Electrochemical Control of Crystals
Authors: Laxmi, S. / Myers, W.K. / Yang, Z.Y. / Seefeldt, L.C. / Carr, S.B. / Vincent, K.A.
History
DepositionApr 8, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Nitrogenase molybdenum-iron protein alpha chain
F: Nitrogenase molybdenum-iron protein beta chain
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
G: Nitrogenase molybdenum-iron protein alpha chain
H: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,21947
Polymers465,5548
Non-polymers8,66439
Water30,6261700
1
E: Nitrogenase molybdenum-iron protein alpha chain
F: Nitrogenase molybdenum-iron protein beta chain
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,09223
Polymers232,7774
Non-polymers4,31419
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
G: Nitrogenase molybdenum-iron protein alpha chain
H: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,12724
Polymers232,7774
Non-polymers4,35020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.055, 156.578, 202.196
Angle α, β, γ (deg.)90.000, 89.977, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 4 through 248 or resid 250 through 608))
d_2ens_1(chain "C" and (resid 4 through 248 or resid 250 through 608))
d_3ens_1(chain "E" and (resid 4 through 248 or resid 250 through 608))
d_4ens_1(chain "G" and (resid 4 through 248 or resid 250 through 608))
d_1ens_2(chain "B" and (resid 2 through 370 or resid 372 through 607))
d_2ens_2(chain "D" and (resid 2 through 370 or resid 372 through 606))
d_3ens_2(chain "F" and (resid 2 through 370 or resid 372 through 607))
d_4ens_2(chain "H" and (resid 2 through 370 or resid 372 through 606))

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_1METMETARGARGAC4 - 24817 - 261
d_12ens_1VALVALGLUGLUAC250 - 480263 - 493
d_13ens_1HCAHCAHCAHCAAT601
d_14ens_1ICSICSICSICSAU602
d_15ens_11CL1CL1CL1CLBW601
d_21ens_1METMETARGARGCE4 - 24817 - 261
d_22ens_1VALVALGLUGLUCE250 - 480263 - 493
d_23ens_1HCAHCAHCAHCACBA601
d_24ens_1ICSICSICSICSCCA602
d_25ens_11CL1CL1CL1CLDGA601
d_31ens_1METMETARGARGEA4 - 24817 - 261
d_32ens_1VALVALGLUGLUEA250 - 480263 - 493
d_33ens_1HCAHCAHCAHCAEI601
d_34ens_1ICSICSICSICSEJ602
d_35ens_11CL1CL1CL1CLFM601
d_41ens_1METMETARGARGGG4 - 24817 - 261
d_42ens_1VALVALGLUGLUGG250 - 480263 - 493
d_43ens_1HCAHCAHCAHCAGNA601
d_44ens_1ICSICSICSICSGOA602
d_45ens_11CL1CL1CL1CLGPA603
d_11ens_2SERSERTRPTRPBD2 - 3702 - 370
d_12ens_2ASPASPARGARGBD372 - 523372 - 523
d_13ens_2GOLGOLGOLGOLEK603
d_14ens_2GOLGOLGOLGOLBX602
d_21ens_2SERSERTRPTRPDF2 - 3702 - 370
d_22ens_2ASPASPARGARGDF372 - 523372 - 523
d_23ens_2GOLGOLGOLGOLDHA602
d_24ens_2GOLGOLGOLGOLDIA603
d_31ens_2SERSERTRPTRPFB2 - 3702 - 370
d_32ens_2ASPASPARGARGFB372 - 523372 - 523
d_33ens_2GOLGOLGOLGOLFN602
d_34ens_2GOLGOLGOLGOLFO603
d_41ens_2SERSERTRPTRPHH2 - 3702 - 370
d_42ens_2ASPASPARGARGHH372 - 523372 - 523
d_43ens_2GOLGOLGOLGOLHRA601
d_44ens_2GOLGOLGOLGOLCEA604

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999995382817, 0.00296497474602, -0.000665785206089), (0.00296588288462, -0.999994667148, 0.00136719219728), (-0.000661727965217, -0.00136916052565, -0.999998843757)22.411604272, -3.25888343343, -101.041615283
2given(-0.999996348125, -0.0026835439756, 0.00031988799923), (-0.00268392585858, 0.999995678968, -0.00119941138417), (-0.000316667943789, -0.00120026555974, -0.999999229542)-64.4927009906, -0.0924213098896, -101.037812226
3given(-0.999999860941, 0.000293098141305, 0.000438420370958), (-0.000293041319489, -0.999999948657, 0.000129664408367), (0.000438458352846, 0.000129535915052, 0.999999895487)-42.069250573, -3.38322442917, 0.0133041058591
4given(0.99999327239, 0.00316469861044, -0.00185468538269), (0.00317003250114, -0.999990828055, 0.00288005202623), (-0.00184555387497, -0.00288591206331, -0.999994132704)22.2993103487, -3.11367456408, -101.028561012
5given(-0.999995582808, -0.00293757589612, 0.000452782632236), (-0.00293864825673, 0.999992835186, -0.00238619406248), (-0.000445769761972, -0.00238751409109, -0.999997050529)-64.4717081759, -0.200862577158, -100.999544693
6given(-0.99999874607, -0.000223516768245, 0.00156776871645), (0.000224032521897, -0.999999920848, 0.000328805146548), (0.0015676950989, 0.000329155965428, 0.999998716993)-41.9624732169, -3.33162253111, 0.0558463109874

-
Components

-
Nitrogenase molybdenum-iron protein ... , 2 types, 8 molecules EACGFBDH

#1: Protein
Nitrogenase molybdenum-iron protein alpha chain / Dinitrogenase / Nitrogenase component I


Mass: 56852.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mo-Nitrogenase, MoFe protein, P2+ redox state, -150 mV
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ2102 / Gene: nifD / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ2102 / References: UniProt: P07328, nitrogenase
#2: Protein
Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59535.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mo-Nitrogenase, MoFe protein, P2+ redox state, -150 mV
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ2102 / Gene: nifK / Production host: Azotobacter vinelandii DJ (bacteria) / Strain (production host): DJ2102 / References: UniProt: P07329, nitrogenase

-
Non-polymers , 7 types, 1739 molecules

#3: Chemical
ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10O7
#4: Chemical
ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1700 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.51 % / Description: Brown Diamond-shaped crystals
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 0.1 M sodium citrate pH 5.0, 0.16 M ammonium acetate, 17% (v/v) PEG Smear High, 25% (v/v) glycerol
PH range: 5-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationMonochromator: 0.95 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.9→156.58 Å / Num. obs: 404327 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 27.93 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.062 / Net I/σ(I): 5.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 19754 / CC1/2: 0.776 / Rpim(I) all: 0.654

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→84.06 Å / SU ML: 0.2087 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 20112 5 %
Rwork0.1821 381897 -
obs0.1832 402009 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31856 0 313 1700 33869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009733023
X-RAY DIFFRACTIONf_angle_d0.982844778
X-RAY DIFFRACTIONf_chiral_restr0.0554672
X-RAY DIFFRACTIONf_plane_restr0.01065728
X-RAY DIFFRACTIONf_dihedral_angle_d15.807812270
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.326029310957
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.311658853488
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.26706583119
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.47803086765
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS0.403729877038
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS2.47872665099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.3616370.358912564X-RAY DIFFRACTION96.74
1.92-1.940.36266400.332412481X-RAY DIFFRACTION96.73
1.94-1.970.33116760.305912540X-RAY DIFFRACTION97.08
1.97-1.990.32587010.303812635X-RAY DIFFRACTION97.1
1.99-2.020.30736660.291312492X-RAY DIFFRACTION97.09
2.02-2.050.28456610.29112615X-RAY DIFFRACTION96.88
2.05-2.080.31816350.274212510X-RAY DIFFRACTION97.2
2.08-2.110.2816270.262212711X-RAY DIFFRACTION97.14
2.11-2.140.27276650.244312561X-RAY DIFFRACTION97.31
2.14-2.170.26186830.231812584X-RAY DIFFRACTION97.3
2.17-2.210.25466520.219512740X-RAY DIFFRACTION97.81
2.21-2.250.22416510.210512645X-RAY DIFFRACTION97.76
2.25-2.30.23656980.200512581X-RAY DIFFRACTION97.68
2.3-2.340.22326140.189612829X-RAY DIFFRACTION97.85
2.34-2.390.22636760.192712672X-RAY DIFFRACTION97.82
2.39-2.450.22266510.190212667X-RAY DIFFRACTION98.01
2.45-2.510.21876300.19312745X-RAY DIFFRACTION98.13
2.51-2.580.22346650.192412787X-RAY DIFFRACTION98.43
2.58-2.650.23256840.195112757X-RAY DIFFRACTION98.39
2.65-2.740.21457160.183212728X-RAY DIFFRACTION98.44
2.74-2.840.227440.179212730X-RAY DIFFRACTION98.73
2.84-2.950.19966610.169712839X-RAY DIFFRACTION98.77
2.95-3.090.19797200.172812828X-RAY DIFFRACTION98.88
3.09-3.250.20056670.173212874X-RAY DIFFRACTION99.03
3.25-3.450.1866280.167212958X-RAY DIFFRACTION99.25
3.45-3.720.18696310.162512972X-RAY DIFFRACTION99.38
3.72-4.090.17396660.144812957X-RAY DIFFRACTION99.4
4.09-4.690.14147430.125612964X-RAY DIFFRACTION99.53
4.69-5.90.13776860.133613001X-RAY DIFFRACTION99.51
5.9-84.060.16697380.158812930X-RAY DIFFRACTION98.19
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57617080782-0.060632169562-0.1012812065720.290898908311-0.0475859779111.09921282824-0.0432698560593-0.0731180056362-0.057852916350.0861986229872-0.0312917551634-0.01457688679740.05090993403660.07863224046370.07101847592770.257613178467-0.01328376503130.01065673032620.2092983047540.03161917367260.298338850705-29.63429.478-15.691
20.398921601586-0.0442786194772-0.0697072592920.313302974896-0.07245952086011.10922951186-0.009611651625490.1183758570980.03506208569340.0141743517873-0.0229106819190.0458212382866-0.171767437168-0.2569388374190.02799035112590.232629798180.0294254797578-0.001158585922490.2878791953680.01627784545770.291477308599-45.11344.197-36.822
30.556634060624-0.0600926584684-0.04014324648050.3163026884410.008950482808341.12317961080.006704470093620.395737396248-0.0762421983105-0.15247757834-0.07031143300620.03901772863620.131201062004-0.06223883398840.06237332562320.3240965096640.0241601758695-0.008918479364260.624063463919-0.04647506507360.289317925086-34.96529.375-85.371
40.370865364911-0.0216301351993-0.05241463581030.252231840031-0.008461326132421.2009965307-0.002660350672060.2217426523870.0501615106-0.0509656059844-0.0604977031008-0.036482957415-0.1962262561070.2684558023060.06354632527990.262620405139-0.03314313447140.002978691135760.4406050560150.07709885206420.286254621988-19.5444.215-64.271
50.577585159331-0.02740451099430.07741628277380.3489859828450.03914461434151.06197047736-0.0413360357835-0.05911226495770.04177070636040.0951784425336-0.02922451729530.0125957880288-0.0419863743802-0.07193040250980.06883851361640.25237440763-0.000191274703768-0.007176036893360.205476229246-0.03356826686710.29121147965-12.409-32.854-15.688
60.394069953024-0.04824902551690.0762772913540.3106365961680.07102388149421.08110089519-0.007525125618750.122581943206-0.03606789559640.0197611670491-0.0237025602409-0.03433209028750.1756078958860.255473407330.02942584742730.2398256378150.03717418566240.002460280623410.287114779134-0.01733468134790.2898196853893.049-47.574-36.816
70.59884259309-0.04120023412480.03385870232570.3088463562830.003526047729451.077862878950.004038926068490.3876053287930.0832706824368-0.148941450192-0.0696270520928-0.0342744987929-0.1269186859670.06725275035330.06171094063020.3293324251620.03621744654070.007761449063110.6299835038550.04538661117050.275651331079-7.133-32.759-85.369
80.371626539823-0.00915049193850.03300512680450.2565008936220.05367268738351.24287919209-0.003895931305070.213950111365-0.0465633408185-0.0381079021348-0.0589692000160.03937695296920.193398002502-0.2645304649760.06416228335330.258033510205-0.0198520974415-0.001083813422780.441037573347-0.07411171822830.287244832122-22.547-47.595-64.259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )E4 - 480
2X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )E601 - 602
3X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN F AND RESID 601:601 )F601
4X-RAY DIFFRACTION2( CHAIN F AND ( RESID 2:523 OR RESID 602:607 ) )F2 - 523
5X-RAY DIFFRACTION2( CHAIN F AND ( RESID 2:523 OR RESID 602:607 ) )F602 - 607
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )A4 - 480
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )A601 - 602
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN B AND RESID 601:601 )B601
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 2:523 OR RESID 602:605 ) ) OR ( CHAIN E AND RESID 603:603 )B2 - 523
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 2:523 OR RESID 602:605 ) ) OR ( CHAIN E AND RESID 603:603 )B602 - 605
11X-RAY DIFFRACTION4( CHAIN B AND ( RESID 2:523 OR RESID 602:605 ) ) OR ( CHAIN E AND RESID 603:603 )E603
12X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )C4 - 480
13X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )C601 - 602
14X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )D601
15X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:523 OR RESID 602:606 ) ) OR ( CHAIN C AND RESID 603:603 )D2 - 523
16X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:523 OR RESID 602:606 ) ) OR ( CHAIN C AND RESID 603:603 )D602 - 606
17X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:523 OR RESID 602:606 ) ) OR ( CHAIN C AND RESID 603:603 )C603
18X-RAY DIFFRACTION7( CHAIN G AND ( RESID 4:480 OR RESID 601:603 ) )G4 - 480
19X-RAY DIFFRACTION7( CHAIN G AND ( RESID 4:480 OR RESID 601:603 ) )G601 - 603
20X-RAY DIFFRACTION8( CHAIN H AND ( RESID 2:523 OR RESID 601:604 ) ) OR ( CHAIN C AND RESID 604:604 )H2 - 523
21X-RAY DIFFRACTION8( CHAIN H AND ( RESID 2:523 OR RESID 601:604 ) ) OR ( CHAIN C AND RESID 604:604 )H601 - 604
22X-RAY DIFFRACTION8( CHAIN H AND ( RESID 2:523 OR RESID 601:604 ) ) OR ( CHAIN C AND RESID 604:604 )C604

+
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