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- PDB-29up: Mo-Nitrogenase, MoFe protein, P2+ redox state, +50 mV -

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Basic information

Entry
Database: PDB / ID: 29up
TitleMo-Nitrogenase, MoFe protein, P2+ redox state, +50 mV
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / Mo-Nitrogenase / MoFe protein / P2+ redox state / +50 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 / DI(HYDROXYETHYL)ETHER / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)474,62051
Polymers465,5548
Non-polymers9,06543
Water22,4831248
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)237,25725
Polymers232,7774
Non-polymers4,48021
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)237,36326
Polymers232,7774
Non-polymers4,58622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.009, 156.853, 202.277
Angle α, β, γ (deg.)90.000, 90.002, 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 236 or resid 238 through 248 or resid 250 through 608))
d_2ens_1(chain "C" and (resid 4 through 236 or resid 238 through 248 or resid 250 through 608))
d_3ens_1(chain "E" and (resid 4 through 236 or resid 238 through 248 or resid 250 through 608))
d_4ens_1(chain "G" and (resid 4 through 236 or resid 238 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_1METMETTRPTRPAC4 - 23617 - 249
d_12ens_1SERSERARGARGAC238 - 248251 - 261
d_13ens_1VALVALGLUGLUAC250 - 480263 - 493
d_14ens_1HCAHCAHCAHCAAT502
d_15ens_1ICSICSICSICSAU503
d_16ens_11CL1CL1CL1CLAV504
d_21ens_1METMETTRPTRPCE4 - 23617 - 249
d_22ens_1SERSERARGARGCE238 - 248251 - 261
d_23ens_1VALVALGLUGLUCE250 - 480263 - 493
d_24ens_1HCAHCAHCAHCACDA601
d_25ens_1ICSICSICSICSCEA602
d_26ens_11CL1CL1CL1CLDHA601
d_31ens_1METMETTRPTRPEA4 - 23617 - 249
d_32ens_1SERSERARGARGEA238 - 248251 - 261
d_33ens_1VALVALGLUGLUEA250 - 480263 - 493
d_34ens_1HCAHCAHCAHCAEI601
d_35ens_1ICSICSICSICSEJ602
d_36ens_11CL1CL1CL1CLEK603
d_41ens_1METMETTRPTRPGG4 - 23617 - 249
d_42ens_1SERSERARGARGGG238 - 248251 - 261
d_43ens_1VALVALGLUGLUGG250 - 480263 - 493
d_44ens_1HCAHCAHCAHCAGPA601
d_45ens_1ICSICSICSICSGQA602
d_46ens_11CL1CL1CL1CLHSA601
d_11ens_2SERSERTRPTRPBD2 - 3702 - 370
d_12ens_2ASPASPARGARGBD372 - 523372 - 523
d_13ens_2GOLGOLGOLGOLBW601
d_14ens_2GOLGOLGOLGOLBX602
d_21ens_2SERSERTRPTRPDF2 - 3702 - 370
d_22ens_2ASPASPARGARGDF372 - 523372 - 523
d_23ens_2GOLGOLGOLGOLDIA602
d_24ens_2GOLGOLGOLGOLDJA603
d_31ens_2SERSERTRPTRPFB2 - 3702 - 370
d_32ens_2ASPASPARGARGFB372 - 523372 - 523
d_33ens_2GOLGOLGOLGOLAS501
d_34ens_2GOLGOLGOLGOLFL601
d_41ens_2SERSERTRPTRPHH2 - 3702 - 370
d_42ens_2ASPASPARGARGHH372 - 523372 - 523
d_43ens_2GOLGOLGOLGOLHTA602
d_44ens_2GOLGOLGOLGOLCFA603

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999999740546, 0.000698200864958, -0.000177268856616), (0.000698319971899, -0.999999529892, 0.000672729495404), (-0.000176799072965, -0.000672853111244, -0.999999758005)22.4387979215, -3.38947748143, -101.097622308
2given(-0.99999960421, -0.000776720698761, 0.000433917887547), (-0.000777047510008, 0.999999414215, -0.000753503601385), (-0.000433332371521, -0.00075384047797, -0.999999621974)-64.4176422719, -0.00504716284553, -101.113588619
3given(-0.999999877489, 0.000271705227988, -0.000413760855886), (-0.000271776828147, -0.999999948104, 0.000173000813122), (-0.000413713829189, 0.000173113242541, 0.999999899436)-42.0412739376, -3.38034425713, -0.00539441642907
4given(0.999999255313, 0.000560986537158, -0.00108382053157), (0.000564162343763, -0.999995542199, 0.00293211574631), (-0.00108217082265, -0.00293272501354, -0.999995114003)22.3614798512, -3.19995563185, -101.051373424
5given(-0.999999799856, -0.000574114746496, 0.00026585664812), (-0.000574770179758, 0.999996779707, -0.00247188493451), (-0.000264436646391, -0.00247203724625, -0.999996909548)-64.4312692078, -0.130336076923, -101.037827882
6given(-0.99999976056, -0.000270400183579, 0.000636996146754), (0.000270833835002, -0.999999731589, 0.000680787717658), (0.000636811890653, 0.000680960074759, 0.999999565382)-41.932104702, -3.31345580812, 0.0179956804254

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Components

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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, +50 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, +50 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

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Non-polymers , 8 types, 1291 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: isolated from a natural source / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.58 % / 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95375 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 1.9→156.81 Å / Num. obs: 402073 / % possible obs: 98 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.081 / Net I/σ(I): 5.3
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 3.03 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 19663 / CC1/2: 0.418 / Rpim(I) all: 1.215 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→67.43 Å / SU ML: 0.2868 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 19944 5 %
Rwork0.1966 378975 -
obs0.1981 398919 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31856 0 341 1248 33445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016833054
X-RAY DIFFRACTIONf_angle_d1.263344810
X-RAY DIFFRACTIONf_chiral_restr0.0694673
X-RAY DIFFRACTIONf_plane_restr0.01365732
X-RAY DIFFRACTIONf_dihedral_angle_d16.38212285
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.31115226703
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.314498768395
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS0.335392349126
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.48233782514
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS0.401306403098
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS2.47251864397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.4236490.436212361X-RAY DIFFRACTION94.83
1.92-1.940.41876120.40612311X-RAY DIFFRACTION95.23
1.94-1.970.39696670.376212403X-RAY DIFFRACTION95.65
1.97-1.990.39126940.377212421X-RAY DIFFRACTION95.72
1.99-2.020.40736440.358412386X-RAY DIFFRACTION95.88
2.02-2.050.34926420.344312529X-RAY DIFFRACTION95.55
2.05-2.080.35626340.31812330X-RAY DIFFRACTION95.6
2.08-2.110.33275950.30512529X-RAY DIFFRACTION95.78
2.11-2.140.30216650.286212434X-RAY DIFFRACTION96.3
2.14-2.170.30077070.268912421X-RAY DIFFRACTION96.27
2.17-2.210.27366280.253212648X-RAY DIFFRACTION96.69
2.21-2.250.28346450.255112515X-RAY DIFFRACTION96.71
2.25-2.30.28876780.242412505X-RAY DIFFRACTION96.86
2.3-2.340.26936340.229312717X-RAY DIFFRACTION97.06
2.34-2.390.26646630.225112612X-RAY DIFFRACTION96.89
2.39-2.450.25036530.213212616X-RAY DIFFRACTION97.23
2.45-2.510.25496190.209212641X-RAY DIFFRACTION97.36
2.51-2.580.23616620.197112716X-RAY DIFFRACTION97.7
2.58-2.650.24846760.194512663X-RAY DIFFRACTION97.76
2.65-2.740.22137090.188812685X-RAY DIFFRACTION97.76
2.74-2.840.23397420.185912662X-RAY DIFFRACTION97.97
2.84-2.950.22366570.180512751X-RAY DIFFRACTION98.07
2.95-3.090.2177220.190712774X-RAY DIFFRACTION98.25
3.09-3.250.21656650.181612839X-RAY DIFFRACTION98.44
3.25-3.450.20716260.174612842X-RAY DIFFRACTION98.73
3.45-3.720.20076200.171812951X-RAY DIFFRACTION98.78
3.72-4.090.18326730.146712928X-RAY DIFFRACTION98.97
4.09-4.690.15967450.124612920X-RAY DIFFRACTION99.13
4.69-5.90.14016790.129712988X-RAY DIFFRACTION99.22
5.9-67.430.16797390.154712877X-RAY DIFFRACTION97.68
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)
10.804972069365-0.0453814543667-0.1579001483120.353412655173-0.00705791761571.45035689831-0.0586455534288-0.0684614334822-0.0742821770380.100837176628-0.0403561695957-0.000822828588190.05957488255860.05881566719590.09815440210670.251126048869-0.01735494521460.004504231897540.1679207048530.01052375603950.30264873818-29.5829.476-15.735
20.491283548899-0.0266020958173-0.1105299668280.352671631315-0.1334513106191.25608847418-0.01145078284580.159226483110.017354419697-0.00398780155736-0.03720493581330.059925796607-0.181639621639-0.3254068783890.0466735346720.2362550784430.0313015579144-0.003899115269960.306038917385-0.02518397397730.295537889716-45.07444.205-36.83
30.591204622547-0.01736872264030.0003854172776430.302422300690.04801040835491.220853390310.005182934655690.412234561672-0.102919268478-0.161998702897-0.08328208537910.03996506427640.171002304813-0.0994651468070.07276363194220.3899500233960.0187837329744-0.003372690060550.727748649522-0.09633010494110.324712024261-34.88329.407-85.398
40.4077397598430.00505683889764-0.03759123002640.300664830869-0.01420124667431.5092395238-0.008119195739470.2728760119270.0353352509344-0.0979373947066-0.0721634306462-0.04483460391-0.2096758025830.2832724405910.08383137829820.278681286427-0.02839648719120.003547498203260.4848631162520.04701896902520.309962340586-19.4344.193-64.302
50.683307846329-0.0194761926530.125271039050.3145217903120.03375941804591.42591435073-0.0577140757669-0.08059206824410.06630392585810.103788442632-0.04704570382520.0113448488847-0.0545518246451-0.06789409696080.09946949378450.25193291805-0.00567193559332-0.006177189588230.168992552296-0.008866077343020.3090633099-12.409-32.878-15.713
60.486452163327-0.07973950492590.1340177649730.4305245545610.0964345921441.51651815423-0.009755441062280.135236398412-0.01271226250160.00516000625547-0.0485236660473-0.0866648633560.2282693966730.3886835790020.06088661855190.2194145319560.04965545147710.00322387266410.3202463903340.03120217989310.2957719242033.065-47.592-36.818
70.609429956952-0.04487147165540.05936524468760.2473378913310.01632687133641.233539073310.006631528726310.4174951193010.119872061995-0.161651319479-0.0855380165382-0.0447317141521-0.177543056940.07670604351320.07532727765450.3925437147340.03975636850240.01384889270280.725552770360.1011916146270.333837541853-7.114-32.792-85.385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:603 ) )E4 - 480
2X-RAY DIFFRACTION1( CHAIN E AND ( RESID 4:480 OR RESID 601:603 ) )E601 - 603
3X-RAY DIFFRACTION2( CHAIN F AND ( RESID 2:523 OR RESID 601:606 ) ) OR ( CHAIN A AND RESID 501:501 )F2 - 523
4X-RAY DIFFRACTION2( CHAIN F AND ( RESID 2:523 OR RESID 601:606 ) ) OR ( CHAIN A AND RESID 501:501 )F601 - 606
5X-RAY DIFFRACTION2( CHAIN F AND ( RESID 2:523 OR RESID 601:606 ) ) OR ( CHAIN A AND RESID 501:501 )A501
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 502:504 ) )A4 - 480
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 4:480 OR RESID 502:504 ) )A502 - 504
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 2:523 OR RESID 601:606 ) )B2 - 523
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 2:523 OR RESID 601:606 ) )B601 - 606
10X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )C4 - 480
11X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )C601 - 602
12X-RAY DIFFRACTION5( CHAIN C AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN D AND RESID 601:601 )D601
13X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:523 OR RESID 602:608 ) )D2 - 523
14X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:523 OR RESID 602:608 ) )D602 - 608
15X-RAY DIFFRACTION7( CHAIN G AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN H AND RESID 601:601 )G4 - 480
16X-RAY DIFFRACTION7( CHAIN G AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN H AND RESID 601:601 )G601 - 602
17X-RAY DIFFRACTION7( CHAIN G AND ( RESID 4:480 OR RESID 601:602 ) ) OR ( CHAIN H AND RESID 601:601 )H601

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