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- PDB-4kh1: The R state structure of E. coli ATCase with CTP,UTP, and Magnesi... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4kh1
TitleThe R state structure of E. coli ATCase with CTP,UTP, and Magnesium bound
Components
  • Aspartate carbamoyltransferase regulatory chain
  • Aspartate carbamoyltransferase
KeywordsTRANSFERASE / pyrimidine nucleotide biosynthesis / feedback inhibition / competing pathway product activation / allostery
Function / homology
Function and homology information


Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal 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
CYTIDINE-5'-TRIPHOSPHATE / N-(PHOSPHONACETYL)-L-ASPARTIC ACID / PHOSPHATE ION / URIDINE 5'-TRIPHOSPHATE / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Kantrowitz, E.R.
CitationJournal: Biochemistry / Year: 2013
Title: New Paradigm for Allosteric Regulation of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Truong, J.K. / Kantrowitz, E.R.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.pdbx_dist_value / _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_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: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,68115
Polymers102,9614
Non-polymers2,71911
Water8,251458
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)317,04245
Polymers308,88412
Non-polymers8,15833
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 area42780 Å2
ΔGint-218 kcal/mol
Surface area98390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.870, 120.870, 154.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Aspartate carbamoyltransferase / / Aspartate transcarbamylase


Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrB, EKO11_4066, KO11_22860 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y328, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrI, EKO11_4067, KO11_22855 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y329, aspartate carbamoyltransferase

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Non-polymers , 7 types, 469 molecules

#3: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO8P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: 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
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.9
Details: 50 mM maleic acid, 1 mM PALA, 3 mM sodium azide, pH 5.9, Microdialysis, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→31.81 Å / Num. all: 66369 / Num. obs: 66369 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.68 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.285.580.4093.41100
2.28-2.375.640.3264.21100
2.37-2.485.650.2595.11100
2.48-2.615.640.1926.51100
2.61-2.775.660.1388.5199.9
2.77-2.995.710.10111.4199.8
2.99-3.295.710.06816.1199.6
3.29-3.765.760.04525199.3
3.76-4.745.770.03135198.6
4.74-31.815.70.02448.2196.6

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.8Ddata reduction
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D09
Resolution: 2.2→31.807 Å / Occupancy max: 1 / Occupancy min: 0.58 / SU ML: 0.23 / σ(F): 0 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 3366 5.07 %
Rwork0.1626 --
obs0.1643 66361 99.34 %
all-66361 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.1597 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 157 458 7747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097432
X-RAY DIFFRACTIONf_angle_d1.06110122
X-RAY DIFFRACTIONf_dihedral_angle_d14.4182788
X-RAY DIFFRACTIONf_chiral_restr0.0731164
X-RAY DIFFRACTIONf_plane_restr0.0051294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23160.28461410.23082607X-RAY DIFFRACTION100
2.2316-2.26490.27141600.23282597X-RAY DIFFRACTION100
2.2649-2.30020.26981470.21522585X-RAY DIFFRACTION100
2.3002-2.33790.25781420.2172627X-RAY DIFFRACTION100
2.3379-2.37820.26821400.21682596X-RAY DIFFRACTION100
2.3782-2.42150.32731200.21612633X-RAY DIFFRACTION100
2.4215-2.4680.24151450.20732595X-RAY DIFFRACTION100
2.468-2.51840.25011350.1962668X-RAY DIFFRACTION100
2.5184-2.57310.2371430.18932604X-RAY DIFFRACTION100
2.5731-2.6330.24171510.18932594X-RAY DIFFRACTION100
2.633-2.69880.23581330.18622606X-RAY DIFFRACTION100
2.6988-2.77170.22121530.1832625X-RAY DIFFRACTION100
2.7717-2.85320.23311240.18492624X-RAY DIFFRACTION100
2.8532-2.94520.22761370.18062638X-RAY DIFFRACTION100
2.9452-3.05040.24441410.18472610X-RAY DIFFRACTION100
3.0504-3.17240.23491390.18172657X-RAY DIFFRACTION100
3.1724-3.31670.24731450.18442596X-RAY DIFFRACTION99
3.3167-3.49130.19571490.16762619X-RAY DIFFRACTION99
3.4913-3.70980.18341460.15012627X-RAY DIFFRACTION99
3.7098-3.99570.17621320.14252637X-RAY DIFFRACTION99
3.9957-4.39690.15991370.13012631X-RAY DIFFRACTION99
4.3969-5.0310.14351510.12532648X-RAY DIFFRACTION98
5.031-6.33030.1571190.16852668X-RAY DIFFRACTION98
6.3303-31.81020.17151360.14822703X-RAY DIFFRACTION95
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)
10.0827-0.29160.07140.2627-0.02810.05880.06350.19430.2150.08-0.14580.5246-0.5893-0.1213-0.00460.36850.0293-0.09070.42890.12310.483435.366243.89753.0733
20.11410.22960.10670.18010.10930.17170.11740.5209-0.0108-0.56120.0250.3852-0.058-0.60040.00030.38870.0374-0.15330.47710.05470.444634.010332.4208-3.0314
30.86730.37-0.11990.9536-0.05390.0087-0.06330.16110.1571-0.10880.137-0.2123-0.06890.03980.02330.3204-0.00770.05440.3340.05540.216750.474136.65712.3218
41.10330.2982-0.04361.63350.14091.11680.0843-0.010.1202-0.04540.04870.113-0.0716-0.0357-00.24490.02890.0150.26150.03210.274448.891142.775512.1359
50.58-0.3542-0.57161.9425-0.12141.0978-0.0519-0.0573-0.1839-0.10120.10420.4892-0.1168-0.190.00340.1871-0.0325-0.03670.38220.10670.48628.321128.222911.724
60.11940.09990.06560.10060.25690.98260.0336-0.60930.19210.29770.17040.6602-0.3002-0.615-0.00270.2850.00860.11440.53540.18490.703421.841332.230621.5072
71.22880.64831.07341.38050.80462.5703-0.30890.4055-0.4610.66090.66040.71250.16790.75750.21960.2263-0.01030.08330.3240.21960.727731.324623.104121.4347
81.25190.0989-0.51593.07760.22190.3552-0.8061-0.6981-0.95491.88420.93061.36860.58430.45850.03960.1334-0.27680.13720.38910.30660.806731.698417.674824.381
90.2355-0.47130.1590.2386-0.10670.09880.0351-0.1784-0.424-0.0370.15180.6437-0.1166-0.26890.00060.2996-0.0103-0.05830.2980.1440.66337.733215.703216.145
101.6926-0.31420.04570.35010.73440.57560.04230.2782-0.0708-0.46090.24570.41610.0394-0.21510.00030.2892-0.0167-0.1010.3533-0.00040.324941.457731.7305-0.0247
110.1790.02940.27560.14420.11570.92810.0473-0.25190.09340.568-0.74070.0008-1.1813-0.2439-0.01780.59130.2414-0.03030.5855-0.12160.669418.119781.876626.4284
120.55850.05550.24010.35180.36290.6958-0.46280.3039-0.16480.17190.1058-0.32060.09080.08-0.00390.59350.1830.01550.5284-0.130.56124.509972.086932.5476
130.09220.0267-0.00640.0843-0.12240.1504-0.4945-0.1678-0.04890.0749-0.45081.07580.8453-0.1858-0.01850.7235-0.02310.18290.8339-0.35850.86179.924671.121836.737
140.4583-0.0560.20050.3907-0.2350.22530.45190.5635-0.1809-0.6291-0.5591-0.1109-0.2986-0.7121-0.00030.60190.26320.02950.6329-0.16140.370522.25572.135123.0874
150.34020.0971-0.190.0486-0.01070.1197-0.05550.1697-0.08650.0738-0.31010.534-0.3363-0.8657-0.00160.5470.2129-0.00580.8417-0.1660.71116.145775.259523.5372
160.11250.04760.08770.4351-0.29750.36360.44840.48180.0478-1.7327-0.4926-0.4679-0.0024-0.4702-0.00330.47870.2006-0.11370.5609-0.15150.647618.322267.152418.9883
170.3785-0.5325-0.04480.77510.00090.2957-0.4056-0.50360.03210.02510.2479-0.07410.1073-0.269800.32140.05420.04020.5301-0.01540.485933.246151.859624.2343
180.152-0.0820.04440.40970.39840.42640.1356-0.3606-0.4006-0.1541-0.43670.68360.2670.0249-0.00130.2553-0.00530.0750.4619-0.03460.644126.824548.547322.325
190.0878-0.0991-0.01940.1182-0.04410.1611-0.4277-0.82640.40410.57880.35280.4508-0.1119-0.07320.00010.5251-0.01710.09720.8063-0.0440.582926.942251.765429.9522
201.22690.25960.28591.33810.03880.99350.0246-0.2390.09490.14750.02680.1326-0.0995-0.142900.32850.02570.03150.3369-0.04990.264459.533654.504878.2347
211.34221.14061.23110.8080.25950.148-0.02360.04130.0611-0.04710.04850.0998-0.01420.0235-00.32040.02370.03520.34070.00570.240853.651247.153967.1279
221.7613-0.2792-0.97840.3838-0.53940.74590.1-0.09760.33480.0416-0.0699-0.0769-0.23780.078-0.00110.4636-0.03470.03560.34710.02590.374270.053866.290867.689
230.3865-0.0210.13670.2540.09410.6559-0.33770.33520.6277-0.97170.19220.4532-0.83330.2626-0.02370.6435-0.001-0.00980.39010.11790.542267.379372.96457.8024
24-0.0068-0.0506-0.23250.30520.00980.5221-0.06810.32820.2726-0.24810.11650.0734-0.00640.25690.00010.5137-0.07230.08020.43340.03680.393274.570862.551457.9311
250.2686-0.4168-0.41542.27540.20941.2989-0.05040.592-0.0018-0.37140.3196-0.4432-0.11240.27540.29060.4963-0.11350.22830.6242-0.00960.404380.299261.878754.9917
260.91010.06870.85171.30740.04890.62010.0281-0.11260.15390.0976-0.0347-0.0949-0.1250.0900.3706-0.01290.03470.3229-0.03190.306473.063954.482971.7017
271.8369-0.2551.27891.88311.37592.1855-0.2996-0.34640.07130.6073-0.04690.07670.0722-0.0286-0.00320.79040.2202-0.02140.5952-0.09640.440925.859379.681447.7201
280.6964-0.43120.62810.9055-0.25921.0808-0.453-0.0157-0.1396-0.4846-0.07340.0308-0.8069-0.1084-0.23370.76480.0755-0.25460.37990.07780.459145.963568.278854.8473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 134 )
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 214 )
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 236 )
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 261 )
9X-RAY DIFFRACTION9chain 'A' and (resid 262 through 284 )
10X-RAY DIFFRACTION10chain 'A' and (resid 285 through 310 )
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 19 )
12X-RAY DIFFRACTION12chain 'B' and (resid 20 through 45 )
13X-RAY DIFFRACTION13chain 'B' and (resid 46 through 57 )
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 76 )
15X-RAY DIFFRACTION15chain 'B' and (resid 77 through 89 )
16X-RAY DIFFRACTION16chain 'B' and (resid 90 through 104 )
17X-RAY DIFFRACTION17chain 'B' and (resid 105 through 130 )
18X-RAY DIFFRACTION18chain 'B' and (resid 131 through 143 )
19X-RAY DIFFRACTION19chain 'B' and (resid 144 through 153 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 53 )
21X-RAY DIFFRACTION21chain 'C' and (resid 54 through 134 )
22X-RAY DIFFRACTION22chain 'C' and (resid 135 through 187 )
23X-RAY DIFFRACTION23chain 'C' and (resid 188 through 215 )
24X-RAY DIFFRACTION24chain 'C' and (resid 216 through 236 )
25X-RAY DIFFRACTION25chain 'C' and (resid 237 through 261 )
26X-RAY DIFFRACTION26chain 'C' and (resid 262 through 310 )
27X-RAY DIFFRACTION27chain 'D' and (resid 11 through 95 )
28X-RAY DIFFRACTION28chain 'D' and (resid 96 through 153 )

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  • 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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