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- PDB-2vzk: Structure of the acyl-enzyme complex of an N-terminal nucleophile... -

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Basic information

Entry
Database: PDB / ID: 2vzk
TitleStructure of the acyl-enzyme complex of an N-terminal nucleophile (Ntn) hydrolase, OAT2
Components
  • (GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ...) x 2
  • GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
KeywordsTRANSFERASE / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE
Function / homology
Function and homology information


glutamate N-acetyltransferase / glutamate N-acetyltransferase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / methione N-acyltransferase activity / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / arginine biosynthetic process / cytoplasm
Similarity search - Function
arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) ...arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glutamate N-acetyltransferase 2 / Arginine biosynthesis bifunctional protein ArgJ 3
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsIqbal, A. / Clifton, I.J. / Schofield, C.J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Anatomy of a Simple Acyl Intermediate in Enzyme Catalysis: Combined Biophysical and Modeling Studies on Ornithine Acetyl Transferase.
Authors: Iqbal, A. / Clifton, I.J. / Bagonis, M. / Kershaw, N.J. / Domene, C. / Claridge, T.D. / Wharton, C.W. / Schofield, C.J.
#1: Journal: Biochem.J. / Year: 2005
Title: X-Ray Crystal Structure of Ornithine Acetyltransferase from the Clavulanic Acid Biosynthesis Gene Cluster.
Authors: Elkins, J.M. / Kershaw, N.J. / Schofield, C.J.
History
DepositionAug 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Polymer sequence
Category: database_PDB_caveat / entity_poly ...database_PDB_caveat / entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp ..._entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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
Revision 3.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,18412
Polymers163,8228
Non-polymers3624
Water5,260292
1
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1684
Polymers40,9242
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-27.2 kcal/mol
Surface area15870 Å2
MethodPISA
2
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)40,9662
Polymers40,9662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-32.1 kcal/mol
Surface area15650 Å2
MethodPISA
3
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0253
Polymers40,9662
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-33.2 kcal/mol
Surface area15060 Å2
MethodPISA
4
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0253
Polymers40,9662
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-33 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.273, 73.878, 172.166
Angle α, β, γ (deg.)90.00, 92.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 180
2111C8 - 180
3111E8 - 180
4111G8 - 180
1121B181 - 336
2121D181 - 336
3121F181 - 336
4121H181 - 336
1221B344 - 390
2221D344 - 390
3221F344 - 390
4221H344 - 390

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999765, -0.020054, -0.008257), (0.020961, 0.991215, 0.13059), (0.005566, -0.130732, 0.991402)-3.872, -26.504, -5.255
2given(0.780333, -0.027043, -0.624779), (-0.038419, -0.999251, -0.004732), (-0.624183, 0.027696, -0.780788)-19.69, 31.746, -67.599
3given(0.764591, -0.019528, -0.64422), (-0.088313, -0.993288, -0.074704), (-0.638437, 0.114011, -0.761183)-23.65, -4.182, -74.933
4given(0.99997, 0.007643, -0.000806), (-0.007489, 0.992572, 0.121428), (0.001728, -0.121419, 0.9926)-4.371, -26.795, -5.511
5given(0.792767, -0.001959, -0.609521), (-0.021425, -0.999466, -0.024653), (-0.609148, 0.032603, -0.792386)-20.499, 31.237, -68.09
6given(0.785642, 0.000687, -0.618682), (-0.072405, -0.993026, -0.093047), (-0.614431, 0.117897, -0.780112)-23.379, -4.809, -75.755

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Components

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Protein , 1 types, 4 molecules ACEG

#1: Protein
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE ACETYL TRANSFERASE / OAT2


Mass: 18089.531 Da / Num. of mol.: 4 / Fragment: RESIDUES 8-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

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GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ... , 2 types, 4 molecules BDFH

#2: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYL TRANSFERASE / OAT2


Mass: 22834.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#3: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYL TRANSFERASE / OAT2


Mass: 22876.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: ACETYLISATION OF THR 181 IN CHAINS D, F, AND H / Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

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Non-polymers , 3 types, 296 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.12 % / Description: NONE
Crystal growTemperature: 290 K / pH: 7.5
Details: 1.4M AMMONIUM SULPHATE, 100MM N-ACETYL-L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 29, 2007 / Details: MONTEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→37 Å / Num. obs: 62183 / % possible obs: 94.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 2.33→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.03 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZ6, CHAIN A

1vz6


Resolution: 2.33→171.5 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 19.81 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL BY TLSANL
RfactorNum. reflection% reflectionSelection details
Rfree0.28432 3048 4.9 %RANDOM
Rwork0.25386 ---
obs0.25538 58750 93.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.038 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-1.98 Å2
2---1 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.33→171.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11211 0 24 292 11527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211380
X-RAY DIFFRACTIONr_bond_other_d0.0030.027538
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.96715443
X-RAY DIFFRACTIONr_angle_other_deg1.331318279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.78551494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57623.478506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.326151795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.53115116
X-RAY DIFFRACTIONr_chiral_restr0.1680.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213022
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022314
X-RAY DIFFRACTIONr_nbd_refined0.2430.22683
X-RAY DIFFRACTIONr_nbd_other0.2210.27955
X-RAY DIFFRACTIONr_nbtor_refined0.1790.25611
X-RAY DIFFRACTIONr_nbtor_other0.0930.26339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.269
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.2261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7681.59491
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.916211904
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81134291
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9094.53539
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2141tight positional0.050.05
12C2141tight positional0.060.05
13E2141tight positional0.050.05
14G2141tight positional0.050.05
21B2421tight positional0.050.05
22D2421tight positional0.060.05
23F2421tight positional0.060.05
24H2421tight positional0.050.05
11A2141tight thermal0.140.5
12C2141tight thermal0.140.5
13E2141tight thermal0.130.5
14G2141tight thermal0.130.5
21B2421tight thermal0.140.5
22D2421tight thermal0.150.5
23F2421tight thermal0.140.5
24H2421tight thermal0.130.5
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 239
Rwork0.337 4521
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)
10.45420.09480.15721.1536-0.19571.42020.0015-0.045-0.05330.0991-0.013-0.08020.06640.08020.01150.04560.0084-0.00570.08870.00850.108819.01623.7028-65.1719
20.4846-0.0133-0.42121.0837-0.28431.4260.0244-0.22140.09060.17150.02530.0435-0.0329-0.0948-0.04970.06230.0154-0.00960.1398-0.02390.08675.20558.9767-63.8503
30.27590.06610.28280.51160.01080.74270.0488-0.1085-0.09260.0832-0.0020.02360.1018-0.0671-0.04680.0763-0.00130.0010.13060.00480.097-1.8682-0.8971-69.5923
41.77070.15690.0020.0809-0.18540.5137-0.0003-0.03020.1226-0.0521-0.01760.0386-0.0634-0.11620.01780.04420.01310.00430.1074-0.00620.113-12.13396.0437-89.597
50.3747-0.1097-0.05010.9949-0.22041.6967-0.0207-0.06570.00720.1327-0.0439-0.0938-0.05840.13180.06470.0722-0.0126-0.01190.10190.00350.098823.170837.3732-55.6437
60.68130.3065-0.3350.30370.51752.85680.0497-0.17890.12630.1164-0.02830.07980.0013-0.0637-0.02150.09360.0055-0.01380.0934-0.02560.08869.596142.5922-53.5583
70.9482-0.11080.83640.5553-0.07561.6990.0252-0.12960.00610.07410.04330.05780.0986-0.1694-0.06850.06160.00450.01570.0998-0.00680.10362.159133.4356-60.1581
81.7219-0.24960.0840.7912-0.41450.87110.03340.020.07240.06340.0280.0257-0.0177-0.1205-0.06140.063-0.00090.00840.09780.01530.1069-8.921742.2359-79.6571
90.9381-0.17060.31120.4144-0.3521.48670.02440.11020.043-0.0637-0.0101-0.09420.01660.1075-0.01430.13830.0122-0.02310.0792-0.00570.098529.726427.2282-25.5777
100.42160.05770.36780.4891-0.06610.46720.09890.0246-0.0338-0.0678-0.07630.19930.1624-0.237-0.02260.158-0.0154-0.0270.1052-0.00330.095118.805621.996-19.6283
110.55250.20930.31840.08440.21031.75020.00910.00850.0508-0.0366-0.04640.074-0.0575-0.22710.03730.1486-0.0089-0.01940.09220.00560.103716.158932.1179-9.5238
120.892-0.4202-0.35230.95410.45581.4861-0.0261-0.03-0.0760.1174-0.02020.120.2357-0.2160.04630.1702-0.0346-0.00370.08210.00120.155621.052525.163110.614
131.30480.15660.66011.1848-0.00611.42550.03070.1354-0.055-0.14320.021-0.09650.06350.1127-0.05170.18980.0091-0.02850.08850.00110.089425.6608-7.2137-34.9708
140.92040.11020.7180.219-0.26521.1591-0.0328-0.0402-0.0916-0.147-0.0048-0.01120.1665-0.20710.03770.225-0.0293-0.05150.0576-0.01410.120215.0879-12.6279-29.9882
150.60340.20620.46350.11110.42272.07440.0095-0.00380.0371-0.0128-0.00280.0571-0.0964-0.2474-0.00670.1461-0.0084-0.02150.09370.03020.113912.6459-3.0196-18.5571
161.0849-0.5182-0.10332.27280.30831.37750.009-0.1437-0.15810.09210.05140.30540.2215-0.2435-0.06040.1505-0.0247-0.01780.12740.02440.141316.9312-11.24991.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 130
2X-RAY DIFFRACTION2A131 - 180
3X-RAY DIFFRACTION3B181 - 284
4X-RAY DIFFRACTION4B285 - 393
5X-RAY DIFFRACTION5C8 - 130
6X-RAY DIFFRACTION6C131 - 180
7X-RAY DIFFRACTION7D182 - 282
8X-RAY DIFFRACTION8D283 - 390
9X-RAY DIFFRACTION9E8 - 127
10X-RAY DIFFRACTION10E128 - 180
11X-RAY DIFFRACTION11F182 - 283
12X-RAY DIFFRACTION12F284 - 392
13X-RAY DIFFRACTION13G8 - 125
14X-RAY DIFFRACTION14G126 - 180
15X-RAY DIFFRACTION15H182 - 283
16X-RAY DIFFRACTION16H284 - 390

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  • 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

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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

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