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- PDB-5odr: Heterodisulfide reductase / [NiFe]-hydrogenase complex from Metha... -

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Basic information

Entry
Database: PDB / ID: 5odr
TitleHeterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 2 minutes.
Components
  • (Heterodisulfide reductase, subunit ...) x 3
  • (Methyl-viologen reducing hydrogenase, subunit ...) x 3
KeywordsOXIDOREDUCTASE / Heterodisulfide reductase / [NiFe]-hydrogenase / FeS cluster / ferredoxin / CCG motif / methanogenesis / flavoprotein / flavin-based electron bifurcation / [2Fe-2S] cluster / macromolecular complex / anaerobic / thioredoxin / metabolism
Function / homology
Function and homology information


dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding ...dihydromethanophenazine:CoB-CoM heterodisulfide reductase / hydrogen dehydrogenase / hydrogen dehydrogenase activity / CoB--CoM heterodisulfide reductase activity / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / hydrogenase (acceptor) / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / 4Fe-4S dicluster domain / : / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / 4Fe-4S dicluster domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Pyridine nucleotide-disulphide oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Coenzyme B ...Non-cubane [4Fe-4S]-cluster / ACETATE ION / 1-THIOETHANESULFONIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / FE2/S2 (INORGANIC) CLUSTER / Chem-NFU / Chem-PE3 / IRON/SULFUR CLUSTER / Coenzyme B / Heterodisulfide reductase, subunit C / Methyl-viologen reducing hydrogenase subunit D / Methyl-viologen reducing hydrogenase subunit G / Methyl-viologen reducing hydrogenase subunit A / Heterodisulfide reductase, subunit B / CoB--CoM heterodisulfide reductase iron-sulfur subunit A
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWagner, T. / Koch, J. / Ermler, U. / Shima, S.
CitationJournal: Science / Year: 2017
Title: Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.
Authors: Wagner, T. / Koch, J. / Ermler, U. / Shima, S.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterodisulfide reductase, subunit A
B: Heterodisulfide reductase, subunit B
C: Heterodisulfide reductase, subunit C
D: Methyl-viologen reducing hydrogenase, subunit D
E: Methyl-viologen reducing hydrogenase, subunit G
F: Methyl-viologen reducing hydrogenase, subunit A
G: Heterodisulfide reductase, subunit A
H: Heterodisulfide reductase, subunit B
I: Heterodisulfide reductase, subunit C
J: Methyl-viologen reducing hydrogenase, subunit D
K: Methyl-viologen reducing hydrogenase, subunit G
L: Methyl-viologen reducing hydrogenase, subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,37465
Polymers451,69812
Non-polymers15,67653
Water19,4561080
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area77770 Å2
ΔGint-874 kcal/mol
Surface area125570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)366.219, 96.920, 134.450
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Heterodisulfide reductase, subunit ... , 3 types, 6 molecules AGBHCI

#1: Protein Heterodisulfide reductase, subunit A


Mass: 71591.672 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TCB9*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#2: Protein Heterodisulfide reductase, subunit B


Mass: 32075.318 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TCB4*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#3: Protein Heterodisulfide reductase, subunit C


Mass: 20483.650 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TC97*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase

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Methyl-viologen reducing hydrogenase, subunit ... , 3 types, 6 molecules DJEKFL

#4: Protein Methyl-viologen reducing hydrogenase, subunit D


Mass: 16057.495 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TC98*PLUS, dihydromethanophenazine:CoB-CoM heterodisulfide reductase
#5: Protein Methyl-viologen reducing hydrogenase, subunit G


Mass: 32511.432 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TC99*PLUS, hydrogenase (acceptor)
#6: Protein Methyl-viologen reducing hydrogenase, subunit A


Mass: 53129.602 Da / Num. of mol.: 2 / Mutation: Wild-type / Source method: isolated from a natural source
Details: The C-terminus has been post-translationally cleaved.
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
References: UniProt: A0A2D0TCA6*PLUS, hydrogenase (acceptor)

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Non-polymers , 13 types, 1133 molecules

#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#11: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#12: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#15: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#16: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H58O15
#17: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#18: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO7PS
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.62 %
Description: Black thick plate square shape of about 0.2 - 0.4 mm length.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, ...Details: All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD and 1 ul of precipitant. Crystal was soaked for 2 minutes in the crystallization solution supplemented with 66 mM of heterodisulfide (CoM-S-S-CoB). Then, the crystal was transferred in a solution containing the mother liquor with 30% glycerol and 10 mM CoM-S-S-CoB prior freezing.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.2→93.36 Å / Num. obs: 224984 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.26 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.096 / Net I/σ(I): 4.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 32472 / CC1/2: 0.563 / Rpim(I) all: 0.496 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ODC

5odc


Resolution: 2.2→90.26 Å / Cor.coef. Fo:Fc: 0.9242 / Cor.coef. Fo:Fc free: 0.9148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 11228 5 %RANDOM
Rwork0.2037 ---
obs0.2048 224629 99.15 %-
Displacement parametersBiso mean: 52.38 Å2
Baniso -1Baniso -2Baniso -3
1-2.5913 Å20 Å27.2812 Å2
2---7.1908 Å20 Å2
3---4.5995 Å2
Refine analyzeLuzzati coordinate error obs: 0.335 Å
Refinement stepCycle: 1 / Resolution: 2.2→90.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61984 0 1676 1080 64740
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00663229HARMONIC4
X-RAY DIFFRACTIONt_angle_deg0.9114882HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d14288SINUSOIDAL5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes821HARMONIC5
X-RAY DIFFRACTIONt_gen_planes9025HARMONIC35
X-RAY DIFFRACTIONt_it63229HARMONIC20
X-RAY DIFFRACTIONt_nbd13SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.1
X-RAY DIFFRACTIONt_other_torsion15.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4133SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact69611SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2337 780 4.74 %
Rwork0.2206 15685 -
all0.2212 16465 -
obs--99.15 %
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)
10.6391-0.38750.07960.017-0.01010.4207-0.1215-0.02320.34470.03170.0499-0.21460.1031-0.1510.0717-0.02270.0569-0.0898-0.1246-0.01550.072333.45158.1466.5975
20.09660.3770.08570.6216-0.13640.1888-0.01150.0933-0.04310.03440.00110.05040-0.04050.0104-0.0533-0.01280.06590.0246-0.11170.020520.4445-38.103317.7807
30.2886-0.1132-0.40190.86910.79190.5127-0.00490.0762-0.00210.07190.0072-0.0001-0.0089-0.026-0.00230.04590.0128-0.00920.0411-0.0039-0.143733.6495-23.40714.9136
40.42470.30650.82871.00430.251.2434-0.0443-0.01410.046-0.0140.0077-0.00920.04560.02310.03660.06140.0566-0.0912-0.0366-0.0797-0.054749.7026-2.40987.8263
50.06270.36140.52960.34350.41041.058-0.0433-0.05560.0722-0.0555-0.02780.15590.03770.03460.0712-0.04930.0933-0.125-0.0363-0.12920.026255.46318.0912117.5119
60.09850.1994-0.00470.71740.1630.5483-0.0203-0.0980.079-0.0219-0.08890.12610.03920.15950.1092-0.11110.0606-0.03230.1401-0.14-0.089373.965113.9776133.5434
70.4258-0.14310.11920.0125-0.20310.3078-0.0595-0.10210.0366-0.01430.0453-0.03940.1373-0.16790.01420.0935-0.0051-0.0096-0.019-0.0219-0.109811.4783-2.639552.4453
81.4715-0.058-0.05680-0.3545-0.1985-0.0007-0.00570.0469-0.00840.0171-0.0424-0.03050.0401-0.0164-0.12290.10660.0130.04990.03020.035678.6121-3.88151.2559
90.8315-0.4393-0.43260.26450.1733-0.15110.0018-0.00210.0019-0.0054-0.0079-0.0077-0.00770.02360.00610.01040.1608-0.0266-0.0092-0.0021-0.005668.5473-21.439652.5324
100.7712-0.3375-0.02430.5822-0.2243-0.0623-0.00450.01-0.01250.01130.00680.01070.01760.0132-0.00230.00580.0705-0.0504-0.01590.0347-0.00182.14244.969424.4327
110.45850.09880.78150.17350.17130.7271-0.01570.00080.03860.0806-0.0084-0.00610.05160.00040.02410.01560.0070.009-0.0680.0531-0.0052-26.985414.122317.2164
120.35770.02860.12780.4690.19990.7192-0.01910.06720.01220.0424-0.13080.07890.1198-0.15520.1499-0.0353-0.05470.046-0.0176-0.0382-0.0172-46.75419.40332.2734
131.2912-1.44490.70580.70530.47991.8016-0.00420.0020.0139-0.0010.0023-0.01570.0087-0.01650.00180.04060.0109-0.00220.03610.00970.044424.20880.51557.8392
140.3095-0.17550.22750.2115-0.15920.1853-0.0333-0.03420.1074-0.00850.026-0.09550.0474-0.03080.00730.0370.0158-0.0552-0.0512-0.0312-0.050922.05653.637860.3514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ V|* }
14X-RAY DIFFRACTION14{ W|* }

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  • 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

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