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- PDB-4fyx: E. coli Aspartate Transcarbamoylase complexed with dCTP, UTP, and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 4fyx
TitleE. coli Aspartate Transcarbamoylase complexed with dCTP, UTP, and Mg2+
Components(Aspartate carbamoyltransferase ...) x 2
KeywordsTRANSFERASE / pyrimidine nucleotide biosynthesis / feedback inhibition / allostery
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular amino acid metabolic process / amino acid binding / nitrogen compound metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / cellular amino acid metabolic process / amino acid binding / nitrogen compound metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase ...Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0889 Å
AuthorsCockrell, G.M. / Kantrowitz, E.R.
CitationJournal: Biochemistry / Year: 2012
Title: Metal Ion Involvement in the Allosteric Mechanism of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Kantrowitz, E.R.
History
DepositionJul 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,04312
Polymers102,9614
Non-polymers2,0828
Water11,422634
1
A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase catalytic chain
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic chain
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,13036
Polymers308,88412
Non-polymers6,24624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area30410 Å2
ΔGint-70 kcal/mol
Surface area104660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.210, 121.210, 141.764
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21C-541-

HOH

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Components

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Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

#1: Protein Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7F3

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Non-polymers , 5 types, 642 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 5.7
Details: 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM dCTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 22.3 % / Av σ(I) over netI: 27.12 / Number: 1599046 / Rmerge(I) obs: 0.145 / Χ2: 1.18 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 71745 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525010010.1141.07328.8
3.594.5210010.0991.321.8
3.143.5910010.1241.29722
2.853.1410010.1651.27222.1
2.652.8510010.2181.25522
2.492.6510010.2731.22421.8
2.372.4910010.3571.15821.6
2.262.3710010.4431.12321.2
2.182.2610010.5461.07720.9
2.12.1810010.6841.01320.3
ReflectionResolution: 2.0889→50 Å / Num. all: 71745 / Num. obs: 71745 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 22.3 % / Rmerge(I) obs: 0.145 / Χ2: 1.178 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.0889-2.1820.30.68471071.0131100
2.18-2.2620.90.54670771.0771100
2.26-2.3721.20.44370921.1231100
2.37-2.4921.60.35771041.1581100
2.49-2.6521.80.27371551.2241100
2.65-2.85220.21871271.2551100
2.85-3.1422.10.16571501.2721100
3.14-3.59220.12471941.2971100
3.59-4.5221.80.09972361.31100
4.52-5028.80.11475031.0731100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZA1
Resolution: 2.0889→49.22 Å / Occupancy max: 1 / Occupancy min: 0.94 / SU ML: 0.26 / σ(F): 0 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 3630 5.06 %Random
Rwork0.1652 ---
obs0.1676 71741 99.95 %-
all-71777 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.269 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso max: 206.07 Å2 / Biso mean: 39.2654 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: LAST / Resolution: 2.0889→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7149 0 118 634 7901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097413
X-RAY DIFFRACTIONf_angle_d1.0710090
X-RAY DIFFRACTIONf_chiral_restr0.0771164
X-RAY DIFFRACTIONf_plane_restr0.0051287
X-RAY DIFFRACTIONf_dihedral_angle_d14.0292771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0889-2.11640.2541300.19752560269099
2.1164-2.14540.2331420.193526032745100
2.1454-2.1760.24651260.187425692695100
2.176-2.20850.24671610.177225902751100
2.2085-2.2430.23861400.176126102750100
2.243-2.27980.25151330.178225712704100
2.2798-2.31910.23251390.177326072746100
2.3191-2.36130.26221510.173825792730100
2.3613-2.40670.22931320.170625882720100
2.4067-2.45580.24951320.164526062738100
2.4558-2.50920.20371370.159426082745100
2.5092-2.56760.2211500.163925812731100
2.5676-2.63180.26471530.169626162769100
2.6318-2.7030.2491350.17926152750100
2.703-2.78250.23031540.177225902744100
2.7825-2.87230.23921430.180925942737100
2.8723-2.97490.25611310.173726182749100
2.9749-3.0940.20411660.178625832749100
3.094-3.23480.22231300.177826332763100
3.2348-3.40530.21521420.166826242766100
3.4053-3.61860.18481170.160926662783100
3.6186-3.89790.20631330.153826562789100
3.8979-4.290.18031430.137426352778100
4.29-4.91020.17211360.131126742810100
4.9102-6.18450.20261330.167727152848100
6.1845-49.23410.18311410.175528202961100
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)
10.28530.1612-0.09820.36870.25970.2715-0.00070.08030.0005-0.11940.0835-0.0117-0.0534-0.070100.19830.013-0.00730.22870.01990.153843.283936.53312.744
20.07380.18810.05470.53630.14530.117-0.0174-0.1284-0.1973-0.0269-0.0277-0.2707-0.1670.0637-0.03140.1687-0.0122-0.0820.28220.06650.131254.877743.378919.0932
30.6560.045-0.01280.4273-0.04610.2547-0.01860.01710.06450.00820.10810.1153-0.0563-0.13530.00390.14120.0166-0.00140.2540.02510.132131.777633.80714.5683
40.0065-0.07610.02630.2314-0.07960.0313-0.02430.0976-0.09560.62630.3840.24950.0062-0.0440.00710.44080.0502-0.0380.34240.010.261134.308822.111829.115
50.468-0.3246-0.1330.34930.2130.1055-0.11460.0786-0.1383-0.10680.0593-0.02310.0765-0.049600.1458-0.0333-0.01430.1820.00060.173837.305821.11469.566
60.17020.25360.00550.4018-0.03110.08690.09470.13730.0634-0.0015-0.1333-0.1467-0.4332-0.3315-0.04680.37710.1705-0.02490.3441-0.07360.310524.028777.860528.9804
70.3270.04980.27570.0480.15190.56230.10680.09660.0047-0.0861-0.17320.0226-0.0625-0.68810.04720.25480.13140.00880.4378-0.09760.314416.5376.172335.9383
80.3366-0.09490.02541.0026-0.00080.00260.06340.03380.0631-0.30730.0918-0.039-0.1608-0.03130.27190.51070.2861-0.03620.3138-0.02790.220723.841579.810522.5972
90.00040.0057-0.00110.0462-0.01770.00130.00450.15720.0328-0.4568-0.12590.2039-0.0471-0.23640.00010.41420.1113-0.03930.428-0.1270.427920.099566.164322.8567
100.57780.2579-0.34640.1599-0.140.2204-0.15390.10640.0704-0.16-0.09140.0367-0.1911-0.2249-0.38960.44370.4785-0.13880.6752-0.2210.346715.911176.379919.4257
110.0339-0.0565-0.05990.05390.09660.07820.0369-0.24750.20770.0646-0.1249-0.0553-0.1026-0.06960.00010.31070.03490.0340.2746-0.03760.260536.104954.578523.9867
120.1458-0.07380.0330.059-0.05850.05770.16760.02140.0487-0.1434-0.02230.12970.1517-0.17520.06120.1830.0028-0.05150.391-0.1030.233121.714951.734321.1416
130.0024-0.0147-0.0050.2899-0.18690.12180.1078-0.0479-0.10080.0728-0.27020.09240.1636-0.1771-0.03040.2138-0.01190.03790.2885-0.10210.21926.314250.706425.7796
140.56150.29520.18230.4082-0.25870.35710.0953-0.1388-0.02540.0986-0.0604-0.041-0.0694-0.037300.1815-0.021-0.00890.1566-0.01020.132863.516352.147267.0385
150.1320.11330.03290.11330.05030.0224-0.0264-0.0385-0.1433-0.05680.196-0.11760.0846-0.13990.00750.2336-0.06240.01750.1986-0.00760.144953.032141.667651.9988
160.73650.3396-0.02650.3792-0.0880.20950.00660.03680.12820.00390.00620.0701-0.0843-0.010200.16490.0015-0.02450.12620.00130.1668.333862.325955.1954
170.2629-0.07140.04680.4185-0.04470.22370.03920.16730.1702-0.261-0.02770.0016-0.07690.23070.05390.295-0.05-0.01210.17810.01130.192680.596759.784847.6916
180.2437-0.0292-0.29390.45920.09170.58190.01150.03850.074-0.3186-0.3834-0.3687-0.37710.1168-0.34480.20510.00850.08290.24190.04620.230687.883858.502547.7064
190.28250.15540.18440.4609-0.16330.2098-0.0155-0.0749-0.2790.0444-0.1425-0.0859-0.01840.0058-0.00080.1891-0.0158-0.02010.1554-0.00160.185575.843251.881262.4925
200.0112-0.0130.00560.0391-0.01350.00060.14640.0610.0563-0.3037-0.17940.0291-0.0821-0.099-0.04030.59210.5307-0.03680.257-0.03550.356221.405290.680640.5664
210.1572-0.08030.11310.0830.07380.15020.17330.03680.04670.0264-0.1034-0.1065-0.3051-0.25050.00050.33940.0742-0.03270.1884-0.01470.317731.187479.304140.5303
220.0132-0.0021-0.00740.0042-0.00050.00150.20810.0184-0.1411-0.21510.1434-0.055-0.16980.22310.00010.4845-0.01420.06810.23620.00840.40535.368790.385832.4108
230.10150.07040.07560.14120.09520.2212-0.115-0.19040.35640.1162-0.0557-0.3058-0.3215-0.217-0.01440.37030.1249-0.06330.2834-0.04790.410932.976684.705447.6915
240.0562-0.22670.16610.0889-0.13480.13410.00260.05630.0637-0.1075-0.1411-0.0149-0.11660.0735-0.02230.24220.0509-0.03660.1863-0.02060.260543.971377.167947.7448
250.1516-0.1146-0.07370.07610.01120.10720.03590.23230.0976-0.2761-0.0023-0.0747-0.0825-0.1415-0.00060.20130.01680.00070.20830.06050.288852.665669.43947.5058
260.0068-0.01230.0070.0108-0.00750.00810.20470.27620.1156-0.23710.0978-0.2349-0.2544-0.31150.00060.2720.03420.01680.30390.14410.327153.28673.221839.576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:66)A1 - 66
2X-RAY DIFFRACTION2chain 'A' and (resseq 67:87)A67 - 87
3X-RAY DIFFRACTION3chain 'A' and (resseq 88:223)A88 - 223
4X-RAY DIFFRACTION4chain 'A' and (resseq 224:247)A224 - 247
5X-RAY DIFFRACTION5chain 'A' and (resseq 248:310)A248 - 310
6X-RAY DIFFRACTION6chain 'B' and (resseq 6:41)B6 - 41
7X-RAY DIFFRACTION7chain 'B' and (resseq 42:57)B42 - 57
8X-RAY DIFFRACTION8chain 'B' and (resseq 58:67)B58 - 67
9X-RAY DIFFRACTION9chain 'B' and (resseq 68:81)B68 - 81
10X-RAY DIFFRACTION10chain 'B' and (resseq 82:101)B82 - 101
11X-RAY DIFFRACTION11chain 'B' and (resseq 102:123)B102 - 123
12X-RAY DIFFRACTION12chain 'B' and (resseq 124:130)B124 - 130
13X-RAY DIFFRACTION13chain 'B' and (resseq 131:153)B131 - 153
14X-RAY DIFFRACTION14chain 'C' and (resseq 1:66)C1 - 66
15X-RAY DIFFRACTION15chain 'C' and (resseq 67:87)C67 - 87
16X-RAY DIFFRACTION16chain 'C' and (resseq 88:217)C88 - 217
17X-RAY DIFFRACTION17chain 'C' and (resseq 218:236)C218 - 236
18X-RAY DIFFRACTION18chain 'C' and (resseq 237:265)C237 - 265
19X-RAY DIFFRACTION19chain 'C' and (resseq 266:310)C266 - 310
20X-RAY DIFFRACTION20chain 'D' and (resseq 6:14)D6 - 14
21X-RAY DIFFRACTION21chain 'D' and (resseq 15:45)D15 - 45
22X-RAY DIFFRACTION22chain 'D' and (resseq 46:57)D46 - 57
23X-RAY DIFFRACTION23chain 'D' and (resseq 58:89)D58 - 89
24X-RAY DIFFRACTION24chain 'D' and (resseq 90:114)D90 - 114
25X-RAY DIFFRACTION25chain 'D' and (resseq 115:143)D115 - 143
26X-RAY DIFFRACTION26chain 'D' and (resseq 144:153)D144 - 153

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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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