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- PDB-3zsf: Crystal structure of the L-cystine solute receptor of Neisseria g... -

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Basic information

Entry
Database: PDB / ID: 3zsf
TitleCrystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the unliganded open conformation
ComponentsABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACIDATP-binding cassette transporter
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amino acid ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesNEISSERIA GONORRHOEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBulut, H. / Moniot, S. / Scheffel, F. / Gathmann, S. / Licht, A. / Saenger, W. / Schneider, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Two Solute Receptors for L-Cystine and L-Cysteine, Respectively, of the Human Pathogen Neisseria Gonorrhoeae.
Authors: Bulut, H. / Moniot, S. / Licht, A. / Scheffel, F. / Gathmann, S. / Saenger, W. / Schneider, E.
History
DepositionJun 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
B: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
C: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
D: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
E: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
F: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
G: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
H: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)240,5398
Polymers240,5398
Non-polymers00
Water10,431579
1
A: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID


Theoretical massNumber of molelcules
Total (without water)30,0671
Polymers30,0671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.090, 99.830, 128.830
Angle α, β, γ (deg.)90.00, 91.50, 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:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 39 - 275 / Label seq-ID: 47 - 283

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
112AA
212CC
312EE
412GG
121BB
221DD
321FF
421HH

NCS ensembles :
ID
1
2

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Components

#1: Protein
ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID / ATP-binding cassette transporter / SOLUTE RECEPTOR FOR L-CYSTINE


Mass: 30067.436 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Strain: FA1090 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q5F9M1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 19 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN E, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN F, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN G, CYS 19 TO ALA ENGINEERED RESIDUE IN CHAIN H, CYS 19 TO ALA
Sequence detailsN-TERMINAL HIS-TAG CONSTRUCT WITH ENTEROKINASE CLEAVAGE SITE AND C19A MUTATION.

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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: 2.31 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 3.5 / Details: 20-30% PEG 3350, 100 MM NA-CITRATE, PH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.32→48 Å / Num. obs: 81031 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.86
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.45 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IEE
Resolution: 2.32→48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.592 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26671 4052 5 %RANDOM
Rwork0.21737 ---
obs0.21981 76978 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.238 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20.31 Å2
2---0.29 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14043 0 0 579 14622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02214318
X-RAY DIFFRACTIONr_bond_other_d0.0020.029315
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.95819410
X-RAY DIFFRACTIONr_angle_other_deg1.068323002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12151895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68926.187577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.558152418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8391538
X-RAY DIFFRACTIONr_chiral_restr0.0890.22257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216227
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022623
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_it0.6591.59377
X-RAY DIFFRACTIONr_mcbond_other0.1611.53918
X-RAY DIFFRACTIONr_mcangle_it1.241214950
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.134941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4994.54460
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
11A1351tight positional0.160.05
12C1351tight positional0.160.05
13E1351tight positional0.150.05
14G1351tight positional0.170.05
21B2760tight positional0.040.05
22D2760tight positional0.040.05
23F2760tight positional0.040.05
24H2760tight positional0.040.05
11A1455medium positional0.280.5
12C1455medium positional0.280.5
13E1455medium positional0.280.5
14G1455medium positional0.30.5
11A1351tight thermal0.580.5
12C1351tight thermal0.520.5
13E1351tight thermal0.580.5
14G1351tight thermal0.560.5
21B2760tight thermal0.110.5
22D2760tight thermal0.110.5
23F2760tight thermal0.110.5
24H2760tight thermal0.110.5
11A1455medium thermal0.672
12C1455medium thermal0.662
13E1455medium thermal0.72
14G1455medium thermal0.642
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 296 -
Rwork0.288 5617 -
obs--100 %
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)
11.8231-0.4228-0.56220.95660.49960.6476-0.00920.2363-0.22880.06350.0781-0.050.01760.0929-0.06890.0878-0.00320.02290.0982-0.04810.19726.167-13.16547.129
26.0034-1.06550.50333.3640.02853.9520.1271-0.06760.7612-0.1151-0.0419-0.171-0.1887-0.1637-0.08530.06340.030.00950.020.01030.28984.7967.38853.028
32.7978-0.9655-0.2221.22090.55140.79750.01160.4421-0.189-0.1435-0.04150.109-0.12770.04520.02990.0926-0.0359-0.00780.1523-0.01450.139420.484-6.33940.279
40.8051-0.1112-0.04430.6682-0.00290.273-0.0347-0.1230.0601-0.03010.0176-0.11840.0071-0.02910.01710.08770.0031-0.00970.0806-0.02520.267526.8843.12769.599
512.67710.7117-3.65974.8779-5.083721.79460.0261.61740.0512-2.235-1.1037-1.60064.48992.34051.07761.39490.76750.69770.66850.33830.570642.7498.76842.34
61.86750.4682-0.46411.68-0.22742.0471-0.0902-0.0560.1937-0.15270.002-0.122-0.15940.02030.08830.07620.0051-0.02130.0028-0.01940.316628.95813.61461.053
71.21750.3042-0.00131.12860.4230.6646-0.07040.1-0.22790.05790.0787-0.05660.0410.054-0.00840.1145-0.00170.02290.1669-0.03790.179726.993-12.989111.977
84.26270.7591-0.71213.5131.04852.8973-0.0453-0.14540.2793-0.2648-0.05920.1768-0.1309-0.10540.10460.09090.0283-0.0760.1096-0.02090.13993.6749.846115.057
92.3229-1.1022-0.97931.13640.60120.6897-0.08850.3109-0.1567-0.0918-0.02560.0794-0.0909-0.02040.11420.1054-0.0486-0.02010.2257-0.01750.086819.737-4.043104.014
101.0776-0.40520.08090.7151-0.15470.6952-0.0669-0.16720.0944-0.02890.0288-0.10660.03060.06190.0380.08890.011-0.02270.2082-0.03050.165826.0026.41132.802
114.2223-0.3995-1.22911.5631-0.07575.16430.00910.15840.2378-0.383-0.123-0.2840.12520.42760.11380.1355-0.02210.06480.1440.05840.167638.46613.377110.187
121.52680.2339-0.27082.1769-0.42550.9671-0.0779-0.0390.267-0.05970.0904-0.1016-0.0657-0.1432-0.01240.10110.0301-0.06580.1791-0.02580.16321.87915.496130.754
131.82920.873-0.35171.9988-0.59090.648-0.01040.09530.17290.080.05620.1073-0.0806-0.0577-0.04580.1110.0281-0.03540.06220.01770.16074.75958.05847.858
144.5653-0.05141.34951.6641-0.70051.90610.02770.1114-0.2942-0.22-0.0108-0.32780.13660.0524-0.0170.09340.01540.04640.0109-0.03540.26626.94537.65947.576
153.29620.1756-1.15611.7556-0.17372.508-0.08740.2085-0.0525-0.0690.0709-0.08930.2017-0.15320.01640.0615-0.0241-0.01670.08210.00080.09966.02752.50538.268
160.6808-0.3224-0.20950.80610.02920.4079-0.0896-0.0971-0.1428-0.02420.04150.0388-0.048-0.01480.0480.09160.0010.01440.10340.03850.22066.36638.55968.47
179.4601-2.1527-0.385911.2931-1.67067.62120.13131.11710.2196-1.049-0.27480.7325-0.6878-0.88530.14350.26290.032-0.10620.4167-0.07180.1273-8.85634.64341.342
181.1483-0.15530.34211.15290.36632.4618-0.0989-0.0383-0.3371-0.12170.00660.11860.1319-0.04490.09220.08720.00730.05520.01550.01320.32594.35128.79260.319
192.14480.27340.22261.6491-0.56680.5471-0.01320.08820.27920.11180.06470.0229-0.0016-0.0184-0.05160.1137-0.0166-0.02270.20450.0270.14053.16860.42112.38
204.76761.020.32884.7965-0.21394.3714-0.02560.1594-0.7032-0.29450.0031-0.34370.19260.10070.02260.08350.01450.03920.1308-0.06060.286626.97937.508114.685
212.5363-1.1610.82781.3564-0.46810.8264-0.01260.2837-0.0806-0.0789-0.0142-0.08850.0969-0.01020.02680.1243-0.05620.00540.2542-0.01330.089810.48651.586104.348
220.5718-0.3196-0.00651.13960.17021.06340.011-0.1019-0.1025-0.10770.02630.142-0.0418-0.0296-0.03730.07280.0025-0.00180.19920.04080.2114.47341.201133.141
233.48131.74162.30585.90394.57885.9093-0.36970.1759-0.0835-1.1914-0.36571.2686-0.852-0.50630.73550.26850.0421-0.26750.1659-0.06730.4315-6.97834.722112.371
243.89041.43240.62553.68470.96090.8901-0.17880.0476-0.3084-0.00740.15940.09240.03410.17950.01950.090.00870.04930.15020.03380.19148.27730.563131.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 150
2X-RAY DIFFRACTION2A151 - 199
3X-RAY DIFFRACTION3A200 - 275
4X-RAY DIFFRACTION4B38 - 141
5X-RAY DIFFRACTION5B142 - 201
6X-RAY DIFFRACTION6B202 - 275
7X-RAY DIFFRACTION7C39 - 137
8X-RAY DIFFRACTION8C138 - 203
9X-RAY DIFFRACTION9C204 - 275
10X-RAY DIFFRACTION10D38 - 146
11X-RAY DIFFRACTION11D147 - 231
12X-RAY DIFFRACTION12D232 - 275
13X-RAY DIFFRACTION13E39 - 136
14X-RAY DIFFRACTION14E137 - 229
15X-RAY DIFFRACTION15E230 - 275
16X-RAY DIFFRACTION16F38 - 145
17X-RAY DIFFRACTION17F146 - 198
18X-RAY DIFFRACTION18F199 - 275
19X-RAY DIFFRACTION19G39 - 137
20X-RAY DIFFRACTION20G138 - 200
21X-RAY DIFFRACTION21G201 - 275
22X-RAY DIFFRACTION22H38 - 145
23X-RAY DIFFRACTION23H146 - 237
24X-RAY DIFFRACTION24H238 - 275

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