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- PDB-4ime: Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic ... -

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Basic information

Entry
Database: PDB / ID: 4ime
TitleCrystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase K164A Mutant
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / Tim barrel / Schiff base
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / Chem-PG6 / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesPasteurella multocida subsp. gallicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsFisher, A.J. / Huynh, N.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Basis for Substrate Specificity and Mechanism of N-Acetyl-d-neuraminic Acid Lyase from Pasteurella multocida.
Authors: Huynh, N. / Aye, A. / Li, Y. / Yu, H. / Cao, H. / Tiwari, V.K. / Shin, D.W. / Chen, X. / Fisher, A.J.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
E: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,90716
Polymers260,6038
Non-polymers1,3048
Water50,1722785
1
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8948
Polymers130,3024
Non-polymers5934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-35 kcal/mol
Surface area41350 Å2
MethodPISA
2
E: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0138
Polymers130,3024
Non-polymers7114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-36 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.140, 147.710, 111.980
Angle α, β, γ (deg.)90.00, 98.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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Components

#1: Protein
N-acetylneuraminate lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid ...N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 32575.414 Da / Num. of mol.: 8 / Mutation: K164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida subsp. gallicida (bacteria)
Strain: P1059 / Gene: nanA, PM1715 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CKB0, N-acetylneuraminate lyase
#2: Chemical
ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H16O3
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2785 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNIPROT SEQUENCE REFERENCE Q9CKB0 IS FOR A DIFFERENT STRAIN (PM70).

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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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% isopropanol, 0.1 M phosphate-citrate, pH 4.5, 1% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2011
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 287971 / Num. obs: 287971 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.292 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.4593736562089597.4
1.8-1.840.3863.75781362077799.3
1.84-1.90.2944.84761262022799.4
1.9-1.960.2415.8739421964699.4
1.96-2.020.2016.9714871898299.4
2.02-2.090.1618.44693911844799.4
2.09-2.170.1359.83667431773799.4
2.17-2.260.11411.47643321714699.3
2.26-2.360.09912.85614211633099.2
2.36-2.470.08814.15588711568099.2
2.47-2.610.07516.09556811487599.1
2.61-2.770.06817.35526541409599.2
2.77-2.960.05619.88493861324299
2.96-3.20.04722.82456651229798.9
3.2-3.50.03926.41418591134198.7
3.5-3.910.03429.82376631025799
3.91-4.520.03232.3533028907598.8
4.52-5.530.03231.728179763598.8
5.53-7.830.03529.4122653600299.5
7.830.02835.5612054328597.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.1982 / WRfactor Rwork: 0.1668 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8807 / SU B: 3.862 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1058 / SU Rfree: 0.1041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 14540 5 %RANDOM
Rwork0.1755 ---
obs0.1771 287943 99.06 %-
all-287943 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.82 Å2 / Biso mean: 17.459 Å2 / Biso min: 2.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.49 Å2
2---0.66 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18360 0 88 2785 21233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01918955
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.98325551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20452372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64525.153819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.731153433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321556
X-RAY DIFFRACTIONr_chiral_restr0.1460.22841
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114079
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1155MEDIUM POSITIONAL0.130.5
2B1155MEDIUM POSITIONAL0.110.5
3C1155MEDIUM POSITIONAL0.110.5
4D1155MEDIUM POSITIONAL0.110.5
5E1155MEDIUM POSITIONAL0.150.5
6F1155MEDIUM POSITIONAL0.140.5
7G1155MEDIUM POSITIONAL0.180.5
8H1155MEDIUM POSITIONAL0.120.5
1A1097LOOSE POSITIONAL0.455
2B1097LOOSE POSITIONAL0.465
3C1097LOOSE POSITIONAL0.55
4D1097LOOSE POSITIONAL0.55
5E1097LOOSE POSITIONAL0.485
6F1097LOOSE POSITIONAL0.595
7G1097LOOSE POSITIONAL0.55
8H1097LOOSE POSITIONAL0.555
1A1155MEDIUM THERMAL1.052
2B1155MEDIUM THERMAL1.932
3C1155MEDIUM THERMAL1.352
4D1155MEDIUM THERMAL2.342
5E1155MEDIUM THERMAL2.442
6F1155MEDIUM THERMAL1.142
7G1155MEDIUM THERMAL2.592
8H1155MEDIUM THERMAL1.182
1A1097LOOSE THERMAL1.6110
2B1097LOOSE THERMAL2.5610
3C1097LOOSE THERMAL2.1510
4D1097LOOSE THERMAL2.9110
5E1097LOOSE THERMAL2.8710
6F1097LOOSE THERMAL1.8210
7G1097LOOSE THERMAL3.2810
8H1097LOOSE THERMAL1.9610
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 1083 -
Rwork0.237 19798 -
all-20881 -
obs--97.42 %
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)
10.5648-0.0643-0.14440.8454-0.06240.82250.00210.00190.00850.0270.06870.115-0.0875-0.119-0.07090.09030.0372-0.04320.11160.02730.10218.124-2.22855.641
20.6245-0.0706-0.09270.4966-0.02760.5104-0.02020.00210.02610.10120.02540.0331-0.0502-0.021-0.00520.12220.0275-0.04770.06720.00080.070623.0514.37657.842
30.56070.07110.34970.449-0.12360.3399-0.0151-0.0679-0.04570.08580.06750.0722-0.0361-0.0745-0.05250.10420.0233-0.04260.10580.02160.076614.866-13.19163.79
40.97921.2267-0.13663.01640.854213.38920.0089-0.0085-0.21440.002-0.09240.27340.5177-0.14970.08350.0718-0.0309-0.04230.11680.0110.27044.36-24.21752.887
50.4925-0.3276-0.21120.6820.06850.48460.02990.0330.06060.0024-0.0272-0.0485-0.017-0.0116-0.00270.09260.0023-0.06560.06450.00990.074638.9857.04331.028
60.2728-0.0772-0.05920.6991-0.10390.31970.01090.0246-0.01580.0067-0.00930.0774-0.0029-0.0046-0.00160.08160.0024-0.06880.07860.0010.068428.372-5.54931.933
70.2593-0.08960.00930.4675-0.04140.03220.0050.01210.0091-0.0124-0.0375-0.0612-0.00710.01820.03260.07890.0032-0.06290.06480.01020.07848.406-4.23834.844
82.8347-1.7337-3.11776.14374.34248.9506-0.0164-0.14230.30470.1990.0104-0.31970.00820.23860.0060.0873-0.0289-0.09340.05650.00680.156556.8659.55844.433
90.887-0.2848-0.17540.4107-0.15810.3248-0.0871-0.0743-0.02320.06890.0580.0094-0.0501-0.02720.02910.13650.0106-0.06660.09540.00370.048745.339-32.24982.802
100.5835-0.10810.14010.3405-0.0660.43630.0065-0.0156-0.04820.03990.02640.0543-0.0337-0.0292-0.03290.1027-0.0027-0.04920.06880.01340.063538.628-38.94169.318
110.5685-0.16560.23120.3495-0.08610.2811-0.0731-0.07270.02180.10090.07050.0432-0.0928-0.06190.00260.14640.0343-0.05690.09540.00130.056735.522-21.31178.84
1212.92871.124-3.86032.6120.66943.5380.0263-0.31130.57320.13860.0227-0.1687-0.21570.2486-0.0490.16390.0195-0.09820.0683-0.03550.10149.24-10.2485.39
130.67160.1007-0.39410.16-0.28260.66140.0064-0.0267-0.04710.0072-0.0508-0.02070.04290.06390.04450.09950.0019-0.05570.06760.00790.069359.204-41.63945.992
140.14960.0172-0.05620.57220.02290.518-0.0167-0.00770.00750.0867-0.0052-0.0614-0.00690.02870.02190.0781-0.0074-0.07150.0790.00520.069861.648-29.01456.228
150.084-0.04030.08280.3401-0.13420.22950.03040.01950.00570.0067-0.027-0.01420.0235-0.0063-0.00330.08060.0005-0.05230.06230.00030.060552.629-30.37238.181
167.3215.499-5.43855.8106-4.57388.3499-0.06250.0911-0.0457-0.22330.08490.23820.2413-0.199-0.02240.0899-0.0133-0.07810.0568-0.01370.091540.826-44.28133.209
170.69510.2035-0.33580.88280.19120.83290.0525-0.0161-0.05370.03610.0397-0.1786-0.02690.1194-0.09220.0388-0.0098-0.06110.0605-0.00430.127927.551-30.7228.508
180.34770.0601-0.01290.57650.09610.5039-0.00480.0049-0.0301-0.06110.0046-0.0793-0.06530.01060.00020.0481-0.0136-0.03320.02660.00570.060414.334-23.931.615
190.41660.02640.20040.52750.13240.5038-0.00230.0313-0.112-0.04140.062-0.162-0.00630.0648-0.05980.04-0.0008-0.0360.0529-0.02530.143923.629-41.651-1.337
203.2888-0.2971-2.82662.9606-0.16412.53890.0574-0.1804-0.3330.18550.0897-0.22610.41310.3185-0.1470.07050.0354-0.09230.05870.00550.201230.758-52.85111.808
210.64620.1492-0.39910.4154-0.2420.55990.031-0.05560.05890.0296-0.03530.0061-0.02550.03510.00430.0566-0.0095-0.04190.0304-0.00620.0491-8.224-20.90922.32
220.5134-0.0033-0.18850.6015-0.02930.27220.0405-0.0597-0.02080.0623-0.0306-0.08920.01320.0242-0.00990.0637-0.0114-0.05790.04510.00930.05511.757-33.64825.042
230.31560.27790.00720.37860.02490.06860.00780.00390.01630.0162-0.026-0.00110.0116-0.0210.01820.0517-0.0006-0.03770.0248-0.00420.041-16.502-32.17616.444
247.58192.6313-4.57744.0649-4.51296.7396-0.0140.27380.2824-0.12550.06730.1738-0.1246-0.1968-0.05340.09910.0129-0.08880.04340.01190.0961-22.369-18.5584.984
250.7532-0.0331-0.1240.69-0.05110.5283-0.0593-0.0618-0.07850.10710.04410.06880.0036-0.03860.01520.07320.008-0.02540.0390.02050.050.42613.19228.192
260.4174-0.07740.03690.5086-0.05650.51230.01290.0034-0.04070.03130.00650.11370.0361-0.0082-0.01940.0423-0.0137-0.03650.01330.01720.075-2.0216.61513.362
270.2415-0.10910.1890.39980.04260.3984-0.0375-0.0407-0.04830.07730.04960.1152-0.0413-0.0714-0.01210.07180.0151-0.01990.04560.01890.076-8.09423.98821.678
2810.96622.357-0.8021.0960.16060.3399-0.0561-0.16750.14950.15010.01790.0412-0.02510.00290.03820.20950.053-0.05740.0512-0.01630.02352.71235.00631.97
290.42050.0028-0.14040.5367-0.35450.42170.0332-0.0181-0.0298-0.0798-0.059-0.00390.04430.05040.02570.06160.0097-0.04630.02530.00310.046624.4264.244-3.199
300.3606-0.0944-0.05930.60960.01480.4743-0.0079-0.0043-0.00230.0553-0.0256-0.02790.00290.04790.03350.0517-0.0059-0.04670.04320.00960.045823.73416.7677.461
310.1195-0.04520.01350.5646-0.07280.30810.04880.0363-0.0194-0.0815-0.0523-0.02580.01250.00550.00350.07110.013-0.0420.02670.00280.037920.25615.494-12.467
328.63446.3159-4.47756.7121-3.49815.1521-0.04710.2344-0.0344-0.30910.14830.1440.2822-0.2502-0.10110.15110.007-0.09620.0395-0.01970.067510.5291.631-20.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 57
2X-RAY DIFFRACTION2A58 - 167
3X-RAY DIFFRACTION3A168 - 277
4X-RAY DIFFRACTION4A278 - 293
5X-RAY DIFFRACTION5B1 - 57
6X-RAY DIFFRACTION6B58 - 167
7X-RAY DIFFRACTION7B168 - 277
8X-RAY DIFFRACTION8B278 - 293
9X-RAY DIFFRACTION9C1 - 57
10X-RAY DIFFRACTION10C58 - 167
11X-RAY DIFFRACTION11C168 - 277
12X-RAY DIFFRACTION12C278 - 293
13X-RAY DIFFRACTION13D1 - 57
14X-RAY DIFFRACTION14D58 - 167
15X-RAY DIFFRACTION15D168 - 277
16X-RAY DIFFRACTION16D278 - 293
17X-RAY DIFFRACTION17E1 - 57
18X-RAY DIFFRACTION18E58 - 167
19X-RAY DIFFRACTION19E168 - 277
20X-RAY DIFFRACTION20E278 - 293
21X-RAY DIFFRACTION21F1 - 57
22X-RAY DIFFRACTION22F58 - 167
23X-RAY DIFFRACTION23F168 - 277
24X-RAY DIFFRACTION24F278 - 293
25X-RAY DIFFRACTION25G1 - 57
26X-RAY DIFFRACTION26G58 - 167
27X-RAY DIFFRACTION27G168 - 277
28X-RAY DIFFRACTION28G278 - 293
29X-RAY DIFFRACTION29H1 - 57
30X-RAY DIFFRACTION30H58 - 167
31X-RAY DIFFRACTION31H168 - 277
32X-RAY DIFFRACTION32H278 - 293

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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