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- PDB-5dib: 2.25 Angstrom resolution crystal structure of betaine aldehyde de... -

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Basic information

Entry
Database: PDB / ID: 5dib
Title2.25 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) Y450L point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / BetB / structural genomics / NAD / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Rossmann fold / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / nucleotide binding / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Betaine-aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHalavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Citation
Journal: To Be Published
Title: 2.25 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) Y450L point mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289
Authors: Halavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
#1: Journal: Appl. Environ. Microbiol. / Year: 2014
Title: Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus.
Authors: Chen, C. / Joo, J.C. / Brown, G. / Stolnikova, E. / Halavaty, A.S. / Savchenko, A. / Anderson, W.F. / Yakunin, A.F.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus.
Authors: Halavaty, A.S. / Rich, R.L. / Chen, C. / Joo, J.C. / Minasov, G. / Dubrovska, I. / Winsor, J.R. / Myszka, D.G. / Duban, M. / Shuvalova, L. / Yakunin, A.F. / Anderson, W.F.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ncs_dom_lim
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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
C: Betaine aldehyde dehydrogenase
D: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,76813
Polymers228,5694
Non-polymers3,1999
Water15,619867
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25790 Å2
ΔGint-130 kcal/mol
Surface area60720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.866, 102.633, 118.243
Angle α, β, γ (deg.)90.00, 104.83, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 49522 - 516
21SERSERBB-20 - 4951 - 516
12LYSLYSAA-20 - 4961 - 517
22LYSLYSCC-20 - 4961 - 517
13SERSERAA1 - 49522 - 516
23SERSERDD-20 - 4951 - 516
14SERSERBB-20 - 4951 - 516
24SERSERCC1 - 49522 - 516
15LYSLYSBB-20 - 4961 - 517
25LYSLYSDD-20 - 4961 - 517
16SERSERCC1 - 49522 - 516
26SERSERDD-20 - 4951 - 516

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Betaine aldehyde dehydrogenase / Betaine-aldehyde dehydrogenase


Mass: 57142.234 Da / Num. of mol.: 4 / Mutation: Y450L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: gbsA, CH51_13935, ERS157365_02065, ERS157366_01277, ERS157367_01590, ERS157368_01276, ERS157369_01327, ERS157370_01780, ERS157371_01447, ERS157372_01660, ERS157373_01815, ERS157374_00943, ...Gene: gbsA, CH51_13935, ERS157365_02065, ERS157366_01277, ERS157367_01590, ERS157368_01276, ERS157369_01327, ERS157370_01780, ERS157371_01447, ERS157372_01660, ERS157373_01815, ERS157374_00943, ERS157376_02019, ERS157379_02102, ERS157380_01277, ERS157381_01481, ERS157382_01327, ERS157383_01276, ERS157384_01683, ERS157385_01328, ERS157386_01590, ERS157387_01983, ERS157388_01278, ERS157389_01857, ERS157390_01571, ERS157391_01874, ERS157393_01280, ERS157394_01487, ERS157395_01059, ERS157409_01038, ERS195389_01428, ERS195391_02004, ERS445052_00785
Plasmid: P15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-magic / References: UniProt: Q9L4P8, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O
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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: BetB23 (Y450L mutant), 7 mg/ml in 10 mM Tris-HCl pH 8.3 500 mM NaCl 5 mM BME 5 mM NAD (co-crystallized) Crystallization: on 11/19/2014; The Classics II Suite (D3): 0.1 M HEPES pH 7. ...Details: Protein: BetB23 (Y450L mutant), 7 mg/ml in 10 mM Tris-HCl pH 8.3 500 mM NaCl 5 mM BME 5 mM NAD (co-crystallized) Crystallization: on 11/19/2014; The Classics II Suite (D3): 0.1 M HEPES pH 7.0 30% (v/v) Jeffamine ED-2001; soaked in crystallization conditions for cryo protection.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2015
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→29.72 Å / Num. obs: 122946 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 9.4
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.05 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mpb

4mpb


Resolution: 2.25→29.72 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.051 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25532 6154 5 %RANDOM
Rwork0.21557 ---
obs0.21757 116530 99.5 %-
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: 29.716 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å20.4 Å2
2---0.48 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15404 0 209 867 16480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916016
X-RAY DIFFRACTIONr_bond_other_d0.0050.0215222
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.97421698
X-RAY DIFFRACTIONr_angle_other_deg1.028335151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.93452004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.29625.446729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.758152787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3391574
X-RAY DIFFRACTIONr_chiral_restr0.1120.22417
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218186
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023484
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A315420.05
12B315420.05
21A313320.06
22C313320.06
31A311430.06
32D311430.06
41B312660.07
42C312660.07
51B313300.07
52D313300.07
61C311840.06
62D311840.06
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 430 -
Rwork0.295 8612 -
obs--99.77 %
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)
15.0201-2.78881.75210.46040.75060.94520.0587-0.0570.4967-0.8915-0.2512-0.2087-0.1464-0.08580.19250.0981-0.03710.00860.3210.03930.589-67.947436.743914.1196
20.4185-0.20060.04660.78360.22370.62680.00880.0640.0578-0.07410.02790.0005-0.0531-0.0883-0.03670.02470.041-0.00450.1650.05260.087-66.091721.186714.4647
30.3227-0.02250.05290.5098-0.1220.32730.0320.0970.0591-0.0194-0.02980.0558-0.0181-0.1636-0.00210.01450.0334-0.01750.19660.01510.0776-69.23259.960417.6157
40.5108-0.20710.1061.5452-0.81231.47990.02270.0730.0340.09880.09610.2228-0.1867-0.264-0.11880.04610.08860.01680.18770.03820.1374-79.743629.598441.9865
50.095-0.0586-0.23760.58190.33470.6648-0.00790.05270.01310.02080.03340.03320.0212-0.1354-0.02550.00760.0209-0.01690.1760.00790.1043-68.82236.708437.6189
62.8044-1.5390.53570.8933-0.28510.107-0.1966-0.1234-0.28190.06230.2220.0761-0.05710.019-0.02540.6757-0.3013-0.06420.5702-0.03060.6883-75.1193-36.181538.7773
70.66450.27410.28380.64430.39750.9764-0.0203-0.0171-0.06070.10710.0374-0.00380.2262-0.2138-0.01710.0906-0.0965-0.00510.19540.01150.1087-73.485-21.606339.4887
80.14770.1034-0.05680.50160.09250.43980.01270.02-0.02460.0009-0.02780.03670.0954-0.22240.01510.0317-0.0629-0.01720.19080.00010.1051-74.2882-10.342535.1882
90.80480.3097-0.32121.3632-0.24721.32580.02790.0991-0.0549-0.0935-0.00940.12690.1777-0.2418-0.01840.081-0.0908-0.03450.1929-0.03960.1035-71.2327-29.79058.8412
100.0444-0.1206-0.07430.36730.25430.85170.00950.0225-0.0016-0.0398-0.00290.0250.076-0.1253-0.00660.026-0.0368-0.02250.1698-0.01220.0964-65.2793-9.64317.0864
110.24310.31931.26160.4571.78467.06860.18530.05190.06230.3191-0.0439-0.00391.1720.0258-0.14140.5287-0.05310.20570.66080.21180.7761-38.5546-25.91263.9085
120.6203-0.12050.26520.1620.12581.30620.0744-0.0453-0.13430.0463-0.0095-0.0590.23160.0682-0.06490.07240.0067-0.08990.10450.0140.2057-36.1422-22.060950.004
130.4337-0.0420.3690.5982-0.37771.1130.0476-0.0164-0.0710.04310.0182-0.10950.0830.1265-0.06590.03630.0383-0.07690.1662-0.04280.1911-31.8446-13.502342.4527
140.7811-0.0690.17251.2657-0.13490.2341-0.0615-0.18480.01790.19470.079-0.1467-0.0328-0.0406-0.01750.07680.0609-0.09570.2417-0.03820.1534-34.84352.59370.8134
150.2468-0.0905-0.28080.29210.2221.0004-0.0138-0.03220.0520.03530.042-0.08140.0440.0328-0.02810.01740.0122-0.05010.1699-0.01640.1678-40.33364.160342.1531
162.7990.2068-0.92380.0284-0.22822.32860.29870.7959-0.22470.04150.05530.0209-0.4652-0.1146-0.35390.4372-0.05380.1390.38880.0270.3271-22.757725.670212.1556
170.89890.0117-0.42370.61140.28310.94040.01170.01910.1123-0.03890.0491-0.1052-0.1880.0595-0.06080.0491-0.0209-0.02040.13260.00820.2013-28.383920.702424.3646
180.27710.1173-0.44420.6119-0.12990.93190.0029-0.02960.08520.01120.0788-0.0972-0.01530.082-0.08170.0207-0.0078-0.05790.2069-0.02850.2208-28.843612.037832.9342
190.60490.1027-0.0731.76670.02710.78450.06680.1288-0.0238-0.0460.0485-0.29540.01290.1875-0.11530.0141-0.00850.00130.2734-0.06920.2071-16.9508-3.30466.7474
200.1731-0.1626-0.1470.37150.29570.72960.00810.0232-0.0190.03490.0371-0.08480.05140.0148-0.04520.0210.007-0.05520.1727-0.03060.1655-35.8195-6.341227.2634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-20 - 6
2X-RAY DIFFRACTION2A7 - 129
3X-RAY DIFFRACTION3A130 - 257
4X-RAY DIFFRACTION4A258 - 381
5X-RAY DIFFRACTION5A382 - 496
6X-RAY DIFFRACTION6B-20 - 6
7X-RAY DIFFRACTION7B7 - 129
8X-RAY DIFFRACTION8B130 - 258
9X-RAY DIFFRACTION9B259 - 367
10X-RAY DIFFRACTION10B368 - 496
11X-RAY DIFFRACTION11C-20 - 5
12X-RAY DIFFRACTION12C6 - 129
13X-RAY DIFFRACTION13C130 - 257
14X-RAY DIFFRACTION14C258 - 404
15X-RAY DIFFRACTION15C405 - 496
16X-RAY DIFFRACTION16D-20 - 5
17X-RAY DIFFRACTION17D6 - 129
18X-RAY DIFFRACTION18D130 - 257
19X-RAY DIFFRACTION19D258 - 396
20X-RAY DIFFRACTION20D397 - 496

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  • 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

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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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