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- PDB-4qje: 1.85 Angstrom resolution crystal structure of apo betaine aldehyd... -

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Basic information

Entry
Database: PDB / ID: 4qje
Title1.85 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-free sulfinic acid form of Cys289
Components(Betaine aldehyde ...) x 2
KeywordsOXIDOREDUCTASE / structural genomics / NAD / Center for Structural Genomics of Infectious / NIAID / National Institute of Allergy and Infectious Diseases / CSGID / Rossmann fold / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


cellular response to chemical stimulus / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Betaine aldehyde dehydrogenase / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)
CitationJournal: Acta Crystallogr.,Sect.D / 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
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)230,36224
Polymers228,6814
Non-polymers1,68220
Water44,5332472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24920 Å2
ΔGint-127 kcal/mol
Surface area61060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.665, 102.929, 118.074
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1036-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSAA4 - 49625 - 517
21LEULEULYSLYSBB4 - 49625 - 517
12LEULEUSERSERAA4 - 49525 - 516
22LEULEUSERSERCC4 - 49525 - 516
13LEULEUSERSERAA4 - 49525 - 516
23LEULEUSERSERDD4 - 49525 - 516
14LEULEUSERSERBB4 - 49525 - 516
24LEULEUSERSERCC4 - 49525 - 516
15LEULEUSERSERBB4 - 49525 - 516
25LEULEUSERSERDD4 - 49525 - 516
16METMETLYSLYSCC1 - 49622 - 517
26METMETLYSLYSDD1 - 49622 - 517

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Betaine aldehyde ... , 2 types, 4 molecules ACDB

#1: Protein Betaine aldehyde dehydrogenase


Mass: 57178.156 Da / Num. of mol.: 3 / Mutation: G234S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: betB, SACOL2628 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Magic
References: UniProt: Q5HCU0, UniProt: A0A0H2X0S3*PLUS, betaine-aldehyde dehydrogenase
#2: Protein Betaine aldehyde dehydrogenase


Mass: 57146.156 Da / Num. of mol.: 1 / Mutation: G234S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: betB, SACOL2628 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Magic
References: UniProt: Q5HCU0, UniProt: A0A0H2X0S3*PLUS, betaine-aldehyde dehydrogenase

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Non-polymers , 5 types, 2492 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2472 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN ...THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, crystallization conditions: PACT Suite (C5): 0.1 M PCB buffer, pH 8.0, 25% w/v PEG1500, VAPOR DIFFUSION, ...Details: 7 mg/mL protein in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 0.5 mM TCEP, crystallization conditions: PACT Suite (C5): 0.1 M PCB buffer, pH 8.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Apr 17, 2014 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 217702 / Num. obs: 217702 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 15.92
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.3 / Num. unique all: 10794 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NI4

4ni4
PDB Unreleased entry


Resolution: 1.85→29.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.266 / SU ML: 0.068 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17537 10934 5 %RANDOM
Rwork0.14971 ---
obs0.151 206767 99.7 %-
all-206767 --
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: 21.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å2-0 Å20.07 Å2
2--0.13 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15344 0 107 2472 17923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916855
X-RAY DIFFRACTIONr_bond_other_d0.0050.0215993
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.96322931
X-RAY DIFFRACTIONr_angle_other_deg1.089337033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37552199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40325.446784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.094152950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4391580
X-RAY DIFFRACTIONr_chiral_restr0.0980.22511
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219753
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023727
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A319680.06
12B319680.06
21A318570.07
22C318570.07
31A317920.07
32D317920.07
41B318340.06
42C318340.06
51B317110.06
52D317110.06
61C323970.06
62D323970.06
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 784 -
Rwork0.238 14864 -
obs-14864 97.64 %
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)
11.59390.1602-1.27661.369-1.05843.66420.1043-0.01080.2390.14610.03880.2533-0.3947-0.2988-0.14310.08640.08880.00930.1156-0.01040.2394172.949225.3492267.9988
20.6381-0.0253-0.30440.4532-0.11390.61710.0434-0.03490.12570.0125-0.00270.0634-0.1199-0.0134-0.04070.02720.0152-0.00120.0466-0.00960.1091191.804518.684265.8703
30.48940.0128-0.10840.47860.16190.73430.0202-0.00550.09870.0106-0.00080.1171-0.0542-0.1103-0.01940.02590.0257-0.02330.08770.01620.1283185.517612.0217257.9076
40.6233-0.0328-0.10791.49550.03710.81450.0104-0.12290.00940.10960.03180.2589-0.0235-0.1517-0.04210.01150.0180.02410.130.03350.1171175.3311-3.4704284.8042
50.45370.2367-0.20310.9486-0.45620.86380.0132-0.059-0.0197-0.00850.00990.06530.0553-0.0522-0.0230.00920.0003-0.01510.06740.01320.0887190.459-7.9333271.9857
60.85850.2664-0.81210.87870.9432.5735-0.17610.26720.0002-0.1370.2143-0.04170.0278-0.0617-0.03820.0549-0.0564-0.02160.20150.01250.0888204.6782.1215229.9703
72.59230.37060.8371.6167-0.61753.12340.07240.2061-0.4094-0.07810.0382-0.16110.4462-0.1195-0.11060.0826-0.0222-0.05260.058-0.05030.1884183.9502-31.3442239.4444
81.09240.43540.40140.31280.01460.65260.00850.1969-0.2149-0.01030.0894-0.05220.09090.0301-0.09780.0307-0.0001-0.03490.0803-0.04780.1298193.9516-20.4981240.8101
90.53930.1460.18690.32790.28540.64060.02970.0767-0.0882-0.03670.01760.01810.0159-0.0565-0.04720.019-0.0086-0.03720.07320.00640.0992188.2596-13.4751248.5242
100.87790.392-0.0261.80480.07280.5554-0.20310.40780.0868-0.23820.1720.1293-0.0549-0.10330.03110.0903-0.1114-0.06610.29970.04920.0727189.78281.7226219.5207
110.8780.37060.06180.7092-0.21741.0517-0.09190.18720.1142-0.030.10550.0872-0.12060.01-0.01350.0363-0.0193-0.04060.09990.02870.0828197.67926.8683237.5192
120.8294-0.3061-1.00950.86670.39471.9663-0.0024-0.14720.02390.14740.0632-0.01710.07220.0593-0.06080.0372-0.0001-0.01930.12840.00650.1049193.3053-2.9569281.7655
130.44351.47591.49589.2234-2.245227.9663-0.07820.0487-0.1005-0.06330.30260.32590.6565-0.2244-0.22440.20.01130.170.0414-0.02430.272234.2904-38.2321247.6249
140.5169-0.162-0.04830.7647-0.06850.70990.0070.0513-0.0579-0.06780.0032-0.03420.15190.1211-0.01020.04910.0528-0.0080.0872-0.02550.0464230.1039-21.19249.3046
150.2967-0.11980.03250.62410.03310.39540.03180.0576-0.0198-0.0018-0.0267-0.07160.06260.1202-0.00510.01340.0295-0.00320.0808-0.00690.0524231.1174-9.8804253.3284
160.57630.0463-0.16491.11470.40561.52480.0225-0.0763-0.11220.15220.0155-0.13610.24150.2034-0.03790.08540.0589-0.03270.08250.030.0821230.595-27.8565280.5103
170.24050.02020.03030.5581-0.46561.42620.0256-0.0357-0.03820.0955-0.01020.013-0.03420.0205-0.01530.02430.0069-0.00460.03580.00220.038219.272-11.7613274.7168
180.21320.53210.03861.72170.05311.136-0.03460.03580.0247-0.21220.07090.1122-0.2067-0.0302-0.03630.08660.0134-0.00280.07920.0320.0855219.055623.7365244.8512
190.4930.13280.08950.6618-0.02390.47890.002-0.04350.07350.0480.0115-0.02-0.08950.0429-0.01350.0247-0.0158-0.00010.0412-0.02690.0384223.895222.7054274.2476
200.27170.06440.04430.69270.15370.22450.0246-0.04420.03680.022-0.0116-0.0788-0.02770.0714-0.0130.0144-0.02-0.01080.0593-0.00710.0449226.881710.5431270.9281
210.6246-0.1413-0.08371.42130.51071.14180.03670.02810.0825-0.18550.042-0.2327-0.21780.16-0.07880.0756-0.05260.04310.06740.01880.1054236.235528.6399245.5604
220.59430.0714-0.41760.591-0.40811.1709-0.01020.06480.0286-0.101-0.0258-0.02180.01570.04310.0360.0232-0.0052-0.00320.03720.00390.0343224.429312.1983246.2357
230.2496-0.56250.04091.6367-0.52790.9642-0.0618-0.0199-0.0477-0.00540.10230.19320.1858-0.041-0.04050.0736-0.0034-0.01330.06360.00850.073214.4124-22.2161274.0304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 45
2X-RAY DIFFRACTION2A46 - 129
3X-RAY DIFFRACTION3A130 - 257
4X-RAY DIFFRACTION4A258 - 401
5X-RAY DIFFRACTION5A402 - 476
6X-RAY DIFFRACTION6A477 - 496
7X-RAY DIFFRACTION7B4 - 23
8X-RAY DIFFRACTION8B24 - 129
9X-RAY DIFFRACTION9B130 - 257
10X-RAY DIFFRACTION10B258 - 401
11X-RAY DIFFRACTION11B402 - 476
12X-RAY DIFFRACTION12B477 - 496
13X-RAY DIFFRACTION13C1 - 6
14X-RAY DIFFRACTION14C7 - 129
15X-RAY DIFFRACTION15C130 - 257
16X-RAY DIFFRACTION16C258 - 401
17X-RAY DIFFRACTION17C402 - 477
18X-RAY DIFFRACTION18C478 - 496
19X-RAY DIFFRACTION19D1 - 129
20X-RAY DIFFRACTION20D130 - 257
21X-RAY DIFFRACTION21D258 - 401
22X-RAY DIFFRACTION22D402 - 476
23X-RAY DIFFRACTION23D477 - 496

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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

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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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